MutationT@ster 2025

NEVER press reload or F5 - unless you want to start from the very beginning.
Input seems to be ok - now mapping the variant to the different transcripts...
Querying Taster for transcript #1: ENST00000406462
Querying Taster for transcript #2: ENST00000441735
Querying Taster for transcript #3: ENST00000645164
Querying Taster for transcript #4: ENST00000446797
Querying Taster for transcript #5: ENST00000675087
Querying Taster for transcript #6: ENST00000676184
Querying Taster for transcript #7: ENST00000675086
Querying Taster for transcript #8: ENST00000674700
Querying Taster for transcript #9: ENST00000674914
Querying Taster for transcript #10: ENST00000264126
Querying Taster for transcript #11: ENST00000642355
Querying Taster for transcript #12: ENST00000690509
MT speed 0.59 s - this script 3.144635 s

Transcript summary:

Permalink

Transcript	Gene symbol	Prediction	Tree vote	Model	Splice site change	Variant type	Protein length	Features at a glance
ENST00000690509	CLCC1	Benign	1\|199	without_aae	No	Deletion	N/A	Homozygous in gnomAD
ENST00000674700	GPSM2	Benign	50\|50	simple_aae	No	Deletion	Deletion of 1 or 2 AA	Amino acid sequence changed Homozygous in gnomAD
ENST00000441735	GPSM2	Benign	51\|49	simple_aae	No	Deletion	Deletion of 1 or 2 AA	Amino acid sequence changed Homozygous in gnomAD
ENST00000406462	GPSM2	Benign	63\|37	simple_aae	No	Deletion	Deletion of 1 or 2 AA	Amino acid sequence changed Homozygous in gnomAD Protein features (might be) affected
ENST00000645164	GPSM2	Benign	63\|37	simple_aae	No	Deletion	Deletion of 1 or 2 AA	Amino acid sequence changed Homozygous in gnomAD Protein features (might be) affected
ENST00000446797	GPSM2	Benign	63\|37	simple_aae	No	Deletion	Deletion of 1 or 2 AA	Amino acid sequence changed Homozygous in gnomAD Protein features (might be) affected
ENST00000675087	GPSM2	Benign	63\|37	simple_aae	No	Deletion	Deletion of 1 or 2 AA	Amino acid sequence changed Homozygous in gnomAD
ENST00000676184	GPSM2	Benign	63\|37	simple_aae	No	Deletion	Deletion of 1 or 2 AA	Amino acid sequence changed Homozygous in gnomAD Protein features (might be) affected
ENST00000674914	GPSM2	Benign	63\|37	simple_aae	No	Deletion	Deletion of 1 or 2 AA	Amino acid sequence changed Homozygous in gnomAD
ENST00000264126(MANE Select)	GPSM2	Benign	63\|37	simple_aae	No	Deletion	Deletion of 1 or 2 AA	Amino acid sequence changed Homozygous in gnomAD Protein features (might be) affected
ENST00000642355	GPSM2	Benign	63\|37	simple_aae	No	Deletion	Deletion of 1 or 2 AA	Amino acid sequence changed Homozygous in gnomAD Protein features (might be) affected
ENST00000675086	GPSM2	Benign	70\|30	simple_aae	No	Deletion	Deletion of 1 or 2 AA	Amino acid sequence changed Homozygous in gnomAD

MutationT@ster 2025

Variant:

1:108922543ACTT>A_12_ENST00000690509

Back to summary table

Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: without_aae
Tree vote: 1|199 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr1:108922544_108922546delCTT (GRCh38)

Gene symbol

CLCC1

Gene constraints

LOEUF: 0.78, LOF (oe): 0.57, misssense (oe): 0.77, synonymous (oe): 0.88 ? (gnomAD)

Ensembl transcript ID

ENST00000690509.1

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Deletion

Gene region

intron

DNA changes

c.*45+12079_*45+12081delAAG
g.40982_40984delAAG

AA changes

N/A

Frameshift

No

Length of protein

N/A

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs35029887
gnomAD	homozygous (-/-)	heterozygous	allele carriers
	>32000	>32000	>32000

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.051	0.004
	1.779	0.007
	-0.709	0
	-0.613	0
(flanking)	3.525	0.07

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

1

Strand

-1

Original gDNA sequence snippet

CATTTTAGGGGGAGTGGAAGAAGTTGTTGTTGAAGCTGTATGG

Altered gDNA sequence snippet

CATTTTAGGGGGAGTGGAAGTTGTTGTTGAAGCTGTATGG

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MLCSLLLCEC LLLVAGYAHD DDWIDPTDML NYDAASGTMR KSQAKYGISG EKDVSPDLSC
ADEISECYHK LDSLTYKIDE CEKKKREDYE SQSNPVFRRY LNKILIEAGK LGLPDENKGD
MHYDAEIILK RETLLEIQKF LNGEDWKPGA LDDALSDILI NFKFHDFETW KWRFEDSFGV
DPYNVLMVLL CLLCIVVLVA TELWTYVRWY TQLRRVLIIS FLFSLGWNWM YLYKLAFAQH
QAEVAKMEPL NNVCAKKMDW TGSIWEWFRS SWTYKDDPCQ KYYELLLVNP IWLVPPTKAL
AVTFTTFVTE PLKHIGKGTG EFIKALMKEI PALLHLPVLI IMALAILSFC YGAGKSVHVL
RHIGGPESEP PQALRPRDRR RQEEIDYRPD GGAGDADFHY RGQMGPTEQG PYAKTYEGRR
EILRERDVDL RFQTGNKSPE VLRAFDVPDA EAREHPTVVP SHKSPVLDTK PKETGGILGE
GTPKESSTES SQSAKPVSGQ DTSGNTEGSP AAEKAQLKSE AAGSPDQGST YSPARGVAGP
RGQDPVSSPC G*

Mutated AA sequence

Position of stopcodon in wt / mu CDS

N/A

Position (AA) of stopcodon in wt / mu AA sequence

N/A

Position of stopcodon in wt / mu cDNA

N/A

Position of start ATG in wt / mu cDNA

268 / 268

Last intron/exon boundary

1968

Theoretical NMD boundary in CDS

1650

Length of CDS

1656

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

40981 / 40985

Chromosomal position

108922543 / 108922547

Speed

0.02 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

Back to summary table

MutationT@ster 2025

Variant:

1:108922543ACTT>A_8_ENST00000674700

Back to summary table

Prediction:

BenignPermalink

Summary:

Amino acid sequence changed
Homozygous in gnomAD

Model: simple_aae
Tree vote: 50|50 (del | benign) ?
Automatic classification due to gnomAD,
tree vote conflicts with the automatic classification ?

Analysed issue

Analysis result

Variant

Chr1:108922544_108922546delCTT (GRCh38)

Gene symbol

GPSM2

Gene constraints

LOEUF: 0.86, LOF (oe): 0.57, misssense (oe): 0.73, synonymous (oe): 0.76 ? (gnomAD)

Ensembl transcript ID

ENST00000674700.1

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Deletion

Gene region

CDS

DNA changes

c.1511_1513delCTT
g.47195_47197delCTT

AA changes

deletion of 1 or 2 AA

AAE:	S505-	?
Score:	-

Frameshift

No

Length of protein

Deletion of 1 or 2 AA

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs35029887
gnomAD	homozygous (-/-)	heterozygous	allele carriers
	>32000	>32000	>32000

Protein conservation

Species	Match	AA	Alignment
Human		505	E	K	N	C	H	T	A	S	T	T	T	S	S	T	P	P	K	M	M	L	K	R	I	Q
mutated	not conserved	505	E	K	N	C	H	T	A	S	T	T	T	-	S	T	P	P	K	M	M	L	K	R	I
Ptroglodytes	no homologue
Mmulatta	no homologue
Fcatus	no homologue
Mmusculus	no homologue
Ggallus	no homologue
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	no homologue

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.051	0.004
	1.779	0.007
	-0.709	0
	-0.613	0
(flanking)	3.525	0.07

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

1

Strand

1

Original gDNA sequence snippet

CCATACAGCTTCAACAACAACTTCTTCCACTCCCCCTAAAATG

Altered gDNA sequence snippet

CCATACAGCTTCAACAACAACTTCCACTCCCCCTAAAATG

Original cDNA sequence snippet

CCATACAGCTTCAACAACAACTTCTTCCACTCCCCCTAAAATG

Altered cDNA sequence snippet

CCATACAGCTTCAACAACAACTTCCACTCCCCCTAAAATG

Wildtype AA sequence

MEASCLELAL EGERLCKSGD CRAGVSFFEA AVQVGTEDLK TLSAIYSQLG NAYFYLHDYA
KALEYHHHDL TLARTIGDQL GEAKASGNLG NTLKVLGNFD EAIVCCQRHL DISRELNDKV
GEARALYNLG NVYHAKGKSF GCPGPQDVGE FPEEVRDALQ AAVDFYEENL SLVTALGDRA
AQGRAFGNLG NTHYLLGNFR DAVIAHEQRL LIAKEFGDKA AERRAYSNLG NAYIFLGEFE
TASEYYKKTL LLARQLKDRA VEAQSCYSLG NTYTLLQDYE KAIDYHLKHL AIAQELNDRI
GEGRACWSLG NAYTALGNHD QAMHFAEKHL EISREVGDKS GELTARLNLS DLQMVLGLSY
STNNSIMSEN TEIDSSLNGV RPKLGRRHSM ENMELMKLTP EKVQNWNSEI LAKQKPLIAK
PSAKLLFVNR LKGKKYKTNS STKVLQDASN SIDHRIPNSQ RKISADTIGD EGFFDLLSRF
QSNRMDDQRC CLQEKNCHTA STTTSSTPPK MMLKRIQIR*

Mutated AA sequence

MEASCLELAL EGERLCKSGD CRAGVSFFEA AVQVGTEDLK TLSAIYSQLG NAYFYLHDYA
KALEYHHHDL TLARTIGDQL GEAKASGNLG NTLKVLGNFD EAIVCCQRHL DISRELNDKV
GEARALYNLG NVYHAKGKSF GCPGPQDVGE FPEEVRDALQ AAVDFYEENL SLVTALGDRA
AQGRAFGNLG NTHYLLGNFR DAVIAHEQRL LIAKEFGDKA AERRAYSNLG NAYIFLGEFE
TASEYYKKTL LLARQLKDRA VEAQSCYSLG NTYTLLQDYE KAIDYHLKHL AIAQELNDRI
GEGRACWSLG NAYTALGNHD QAMHFAEKHL EISREVGDKS GELTARLNLS DLQMVLGLSY
STNNSIMSEN TEIDSSLNGV RPKLGRRHSM ENMELMKLTP EKVQNWNSEI LAKQKPLIAK
PSAKLLFVNR LKGKKYKTNS STKVLQDASN SIDHRIPNSQ RKISADTIGD EGFFDLLSRF
QSNRMDDQRC CLQEKNCHTA STTTSTPPKM MLKRIQIR*

Position of stopcodon in wt / mu CDS

1560 / 1557

Position (AA) of stopcodon in wt / mu AA sequence

520 / 519

Position of stopcodon in wt / mu cDNA

1787 / 1784

Position of start ATG in wt / mu cDNA

228 / 228

Last intron/exon boundary

1770

Theoretical NMD boundary in CDS

1492

Length of CDS

1560

Coding sequence (CDS) position

1510 / 1514

cDNA position

1737 / 1741

gDNA position

47194 / 47198

Chromosomal position

108922543 / 108922547

Speed

0.05 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

Back to summary table

MutationT@ster 2025

Variant:

1:108922543ACTT>A_2_ENST00000441735

Back to summary table

Prediction:

BenignPermalink

Summary:

Amino acid sequence changed
Homozygous in gnomAD

Model: simple_aae
Tree vote: 51|49 (del | benign) ?
Automatic classification due to gnomAD,
tree vote conflicts with the automatic classification ?

Analysed issue

Analysis result

Variant

Chr1:108922544_108922546delCTT (GRCh38)

Gene symbol

GPSM2

Gene constraints

LOEUF: 0.83, LOF (oe): 0.55, misssense (oe): 0.77, synonymous (oe): 0.74 ? (gnomAD)

Ensembl transcript ID

ENST00000441735.2

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Deletion

Gene region

CDS

DNA changes

c.1568_1570delCTT
g.47195_47197delCTT

AA changes

deletion of 1 or 2 AA

AAE:	S524-	?
Score:	-

Frameshift

No

Length of protein

Deletion of 1 or 2 AA

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs35029887
gnomAD	homozygous (-/-)	heterozygous	allele carriers
	>32000	>32000	>32000

Protein conservation

Species	Match	AA	Alignment
Human		524	E	K	N	C	H	T	A	S	T	T	T	S	S	T	P	P	K	M	M	L	K	T	S	S
mutated	not conserved	524	E	K	N	C	H	T	A	S	T	T	T	-	S	T	P	P	K	M	M	L	K	T	S
Ptroglodytes	no homologue
Mmulatta	no homologue
Fcatus	no homologue
Mmusculus	no homologue
Ggallus	no homologue
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	no homologue

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.051	0.004
	1.779	0.007
	-0.709	0
	-0.613	0
(flanking)	3.525	0.07

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

1

Strand

1

Original gDNA sequence snippet

CCATACAGCTTCAACAACAACTTCTTCCACTCCCCCTAAAATG

Altered gDNA sequence snippet

CCATACAGCTTCAACAACAACTTCCACTCCCCCTAAAATG

Original cDNA sequence snippet

CCATACAGCTTCAACAACAACTTCTTCCACTCCCCCTAAAATG

Altered cDNA sequence snippet

CCATACAGCTTCAACAACAACTTCCACTCCCCCTAAAATG

Wildtype AA sequence

MEENLISMRE DHSFHVRYRM EASCLELALE GERLCKSGDC RAGVSFFEAA VQVGTEDLKT
LSAIYSQLGN AYFYLHDYAK ALEYHHHDLT LARTIGDQLG EAKASGNLGN TLKVLGNFDE
AIVCCQRHLD ISRELNDKVG EARALYNLGN VYHAKGKSFG CPGPQDVGEF PEEVRDALQA
AVDFYEENLS LVTALGDRAA QGRAFGNLGN THYLLGNFRD AVIAHEQRLL IAKEFGDKAA
ERRAYSNLGN AYIFLGEFET ASEYYKKTLL LARQLKDRAV EAQSCYSLGN TYTLLQDYEK
AIDYHLKHLA IAQELNDRIG EGRACWSLGN AYTALGNHDQ AMHFAEKHLE ISREVGDKSG
ELTARLNLSD LQMVLGLSYS TNNSIMSENT EIDSSLNGVR PKLGRRHSME NMELMKLTPE
KVQNWNSEIL AKQKPLIAKP SAKLLFVNRL KGKKYKTNSS TKVLQDASNS IDHRIPNSQR
KISADTIGDE GFFDLLSRFQ SNRMDDQRCC LQEKNCHTAS TTTSSTPPKM MLKTSSVPVV
SPNTDEFLDL LASSQSRRLD DQRASFSNLP GLRLTQNSQS VLSHLMTNDN KEADEDFFDI
LVKCQVCLYI FFVLHTAQIP LKTLVVL*

Mutated AA sequence

MEENLISMRE DHSFHVRYRM EASCLELALE GERLCKSGDC RAGVSFFEAA VQVGTEDLKT
LSAIYSQLGN AYFYLHDYAK ALEYHHHDLT LARTIGDQLG EAKASGNLGN TLKVLGNFDE
AIVCCQRHLD ISRELNDKVG EARALYNLGN VYHAKGKSFG CPGPQDVGEF PEEVRDALQA
AVDFYEENLS LVTALGDRAA QGRAFGNLGN THYLLGNFRD AVIAHEQRLL IAKEFGDKAA
ERRAYSNLGN AYIFLGEFET ASEYYKKTLL LARQLKDRAV EAQSCYSLGN TYTLLQDYEK
AIDYHLKHLA IAQELNDRIG EGRACWSLGN AYTALGNHDQ AMHFAEKHLE ISREVGDKSG
ELTARLNLSD LQMVLGLSYS TNNSIMSENT EIDSSLNGVR PKLGRRHSME NMELMKLTPE
KVQNWNSEIL AKQKPLIAKP SAKLLFVNRL KGKKYKTNSS TKVLQDASNS IDHRIPNSQR
KISADTIGDE GFFDLLSRFQ SNRMDDQRCC LQEKNCHTAS TTTSTPPKMM LKTSSVPVVS
PNTDEFLDLL ASSQSRRLDD QRASFSNLPG LRLTQNSQSV LSHLMTNDNK EADEDFFDIL
VKCQVCLYIF FVLHTAQIPL KTLVVL*

Position of stopcodon in wt / mu CDS

1884 / 1881

Position (AA) of stopcodon in wt / mu AA sequence

628 / 627

Position of stopcodon in wt / mu cDNA

2300 / 2297

Position of start ATG in wt / mu cDNA

417 / 417

Last intron/exon boundary

2016

Theoretical NMD boundary in CDS

1549

Length of CDS

1884

Coding sequence (CDS) position

1567 / 1571

cDNA position

1983 / 1987

gDNA position

47194 / 47198

Chromosomal position

108922543 / 108922547

Speed

0.05 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

Back to summary table

MutationT@ster 2025

Variant:

1:108922543ACTT>A_1_ENST00000406462

Back to summary table

Prediction:

BenignPermalink

Summary:

Amino acid sequence changed
Homozygous in gnomAD
Protein features (might be) affected

Model: simple_aae
Tree vote: 63|37 (del | benign) ?
Automatic classification due to gnomAD,
tree vote conflicts with the automatic classification ?

Analysed issue

Analysis result

Variant

Chr1:108922544_108922546delCTT (GRCh38)

Gene symbol

GPSM2

Gene constraints

LOEUF: 0.86, LOF (oe): 0.60, misssense (oe): 0.80, synonymous (oe): 0.77 ? (gnomAD)

Ensembl transcript ID

ENST00000406462.6

Genbank transcript ID

UniProt / AlphaMissense peptide

GPSM2_HUMAN | AlphaMissense: transcript, gene

Variant type

Deletion

Gene region

CDS

DNA changes

c.1568_1570delCTT
g.47195_47197delCTT

AA changes

deletion of 1 or 2 AA

AAE:	S524-	?
Score:	-

Frameshift

No

Length of protein

Deletion of 1 or 2 AA

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs35029887
gnomAD	homozygous (-/-)	heterozygous	allele carriers
	>32000	>32000	>32000

Protein conservation

Species	Match	AA	Alignment
Human		524	E	K	N	C	H	T	A	S	T	T	T	S	S	T	P	P	K	M	M	L	K	T	S	S
mutated	not conserved	524	E	K	N	C	H	T	A	S	T	T	T	-	S	T	P	P	K	M	M	L	K	T	S
Ptroglodytes	no homologue
Mmulatta	no homologue
Fcatus	no homologue
Mmusculus	no homologue
Ggallus	no homologue
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	no homologue

Protein features

Start (aa)	End (aa)	Feature	Details
1	684	CHAIN		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.051	0.004
	1.779	0.007
	-0.709	0
	-0.613	0
(flanking)	3.525	0.07

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

1

Strand

1

Original gDNA sequence snippet

CCATACAGCTTCAACAACAACTTCTTCCACTCCCCCTAAAATG

Altered gDNA sequence snippet

CCATACAGCTTCAACAACAACTTCCACTCCCCCTAAAATG

Original cDNA sequence snippet

CCATACAGCTTCAACAACAACTTCTTCCACTCCCCCTAAAATG

Altered cDNA sequence snippet

CCATACAGCTTCAACAACAACTTCCACTCCCCCTAAAATG

Wildtype AA sequence

MEENLISMRE DHSFHVRYRM EASCLELALE GERLCKSGDC RAGVSFFEAA VQVGTEDLKT
LSAIYSQLGN AYFYLHDYAK ALEYHHHDLT LARTIGDQLG EAKASGNLGN TLKVLGNFDE
AIVCCQRHLD ISRELNDKVG EARALYNLGN VYHAKGKSFG CPGPQDVGEF PEEVRDALQA
AVDFYEENLS LVTALGDRAA QGRAFGNLGN THYLLGNFRD AVIAHEQRLL IAKEFGDKAA
ERRAYSNLGN AYIFLGEFET ASEYYKKTLL LARQLKDRAV EAQSCYSLGN TYTLLQDYEK
AIDYHLKHLA IAQELNDRIG EGRACWSLGN AYTALGNHDQ AMHFAEKHLE ISREVGDKSG
ELTARLNLSD LQMVLGLSYS TNNSIMSENT EIDSSLNGVR PKLGRRHSME NMELMKLTPE
KVQNWNSEIL AKQKPLIAKP SAKLLFVNRL KGKKYKTNSS TKVLQDASNS IDHRIPNSQR
KISADTIGDE GFFDLLSRFQ SNRMDDQRCC LQEKNCHTAS TTTSSTPPKM MLKTSSVPVV
SPNTDEFLDL LASSQSRRLD DQRASFSNLP GLRLTQNSQS VLSHLMTNDN KEADEDFFDI
LVKCQGSRLD DQRCAPPPAT TKGPTVPDED FFSLILRSQG KRMDEQRVLL QRDQNRDTDF
GLKDFLQNNA LLEFKNSGKK SADH*

Mutated AA sequence

MEENLISMRE DHSFHVRYRM EASCLELALE GERLCKSGDC RAGVSFFEAA VQVGTEDLKT
LSAIYSQLGN AYFYLHDYAK ALEYHHHDLT LARTIGDQLG EAKASGNLGN TLKVLGNFDE
AIVCCQRHLD ISRELNDKVG EARALYNLGN VYHAKGKSFG CPGPQDVGEF PEEVRDALQA
AVDFYEENLS LVTALGDRAA QGRAFGNLGN THYLLGNFRD AVIAHEQRLL IAKEFGDKAA
ERRAYSNLGN AYIFLGEFET ASEYYKKTLL LARQLKDRAV EAQSCYSLGN TYTLLQDYEK
AIDYHLKHLA IAQELNDRIG EGRACWSLGN AYTALGNHDQ AMHFAEKHLE ISREVGDKSG
ELTARLNLSD LQMVLGLSYS TNNSIMSENT EIDSSLNGVR PKLGRRHSME NMELMKLTPE
KVQNWNSEIL AKQKPLIAKP SAKLLFVNRL KGKKYKTNSS TKVLQDASNS IDHRIPNSQR
KISADTIGDE GFFDLLSRFQ SNRMDDQRCC LQEKNCHTAS TTTSTPPKMM LKTSSVPVVS
PNTDEFLDLL ASSQSRRLDD QRASFSNLPG LRLTQNSQSV LSHLMTNDNK EADEDFFDIL
VKCQGSRLDD QRCAPPPATT KGPTVPDEDF FSLILRSQGK RMDEQRVLLQ RDQNRDTDFG
LKDFLQNNAL LEFKNSGKKS ADH*

Position of stopcodon in wt / mu CDS

2055 / 2052

Position (AA) of stopcodon in wt / mu AA sequence

685 / 684

Position of stopcodon in wt / mu cDNA

2828 / 2825

Position of start ATG in wt / mu cDNA

774 / 774

Last intron/exon boundary

2588

Theoretical NMD boundary in CDS

1764

Length of CDS

2055

Coding sequence (CDS) position

1567 / 1571

cDNA position

2340 / 2344

gDNA position

47194 / 47198

Chromosomal position

108922543 / 108922547

Speed

0.06 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

Back to summary table

MutationT@ster 2025

Variant:

1:108922543ACTT>A_3_ENST00000645164

Back to summary table

Prediction:

BenignPermalink

Summary:

Amino acid sequence changed
Homozygous in gnomAD
Protein features (might be) affected

Model: simple_aae
Tree vote: 63|37 (del | benign) ?
Automatic classification due to gnomAD,
tree vote conflicts with the automatic classification ?

Analysed issue

Analysis result

Variant

Chr1:108922544_108922546delCTT (GRCh38)

Gene symbol

GPSM2

Gene constraints

LOEUF: 0.86, LOF (oe): 0.60, misssense (oe): 0.80, synonymous (oe): 0.77 ? (gnomAD)

Ensembl transcript ID

ENST00000645164.2

Genbank transcript ID

UniProt / AlphaMissense peptide

GPSM2_HUMAN | AlphaMissense: transcript, gene

Variant type

Deletion

Gene region

CDS

DNA changes

c.1568_1570delCTT
g.47195_47197delCTT

AA changes

deletion of 1 or 2 AA

AAE:	S524-	?
Score:	-

Frameshift

No

Length of protein

Deletion of 1 or 2 AA

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs35029887
gnomAD	homozygous (-/-)	heterozygous	allele carriers
	>32000	>32000	>32000

Protein conservation

Species	Match	AA	Alignment
Human		524	E	K	N	C	H	T	A	S	T	T	T	S	S	T	P	P	K	M	M	L	K	T	S	S
mutated	not conserved	524	E	K	N	C	H	T	A	S	T	T	T	-	S	T	P	P	K	M	M	L	K	T	S
Ptroglodytes	no homologue
Mmulatta	no homologue
Fcatus	no homologue
Mmusculus	no homologue
Ggallus	no homologue
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	no homologue

Protein features

Start (aa)	End (aa)	Feature	Details
1	684	CHAIN		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.051	0.004
	1.779	0.007
	-0.709	0
	-0.613	0
(flanking)	3.525	0.07

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

1

Strand

1

Original gDNA sequence snippet

CCATACAGCTTCAACAACAACTTCTTCCACTCCCCCTAAAATG

Altered gDNA sequence snippet

CCATACAGCTTCAACAACAACTTCCACTCCCCCTAAAATG

Original cDNA sequence snippet

CCATACAGCTTCAACAACAACTTCTTCCACTCCCCCTAAAATG

Altered cDNA sequence snippet

CCATACAGCTTCAACAACAACTTCCACTCCCCCTAAAATG

Wildtype AA sequence

MEENLISMRE DHSFHVRYRM EASCLELALE GERLCKSGDC RAGVSFFEAA VQVGTEDLKT
LSAIYSQLGN AYFYLHDYAK ALEYHHHDLT LARTIGDQLG EAKASGNLGN TLKVLGNFDE
AIVCCQRHLD ISRELNDKVG EARALYNLGN VYHAKGKSFG CPGPQDVGEF PEEVRDALQA
AVDFYEENLS LVTALGDRAA QGRAFGNLGN THYLLGNFRD AVIAHEQRLL IAKEFGDKAA
ERRAYSNLGN AYIFLGEFET ASEYYKKTLL LARQLKDRAV EAQSCYSLGN TYTLLQDYEK
AIDYHLKHLA IAQELNDRIG EGRACWSLGN AYTALGNHDQ AMHFAEKHLE ISREVGDKSG
ELTARLNLSD LQMVLGLSYS TNNSIMSENT EIDSSLNGVR PKLGRRHSME NMELMKLTPE
KVQNWNSEIL AKQKPLIAKP SAKLLFVNRL KGKKYKTNSS TKVLQDASNS IDHRIPNSQR
KISADTIGDE GFFDLLSRFQ SNRMDDQRCC LQEKNCHTAS TTTSSTPPKM MLKTSSVPVV
SPNTDEFLDL LASSQSRRLD DQRASFSNLP GLRLTQNSQS VLSHLMTNDN KEADEDFFDI
LVKCQGSRLD DQRCAPPPAT TKGPTVPDED FFSLILRSQG KRMDEQRVLL QRDQNRDTDF
GLKDFLQNNA LLEFKNSGKK SADH*

Mutated AA sequence

MEENLISMRE DHSFHVRYRM EASCLELALE GERLCKSGDC RAGVSFFEAA VQVGTEDLKT
LSAIYSQLGN AYFYLHDYAK ALEYHHHDLT LARTIGDQLG EAKASGNLGN TLKVLGNFDE
AIVCCQRHLD ISRELNDKVG EARALYNLGN VYHAKGKSFG CPGPQDVGEF PEEVRDALQA
AVDFYEENLS LVTALGDRAA QGRAFGNLGN THYLLGNFRD AVIAHEQRLL IAKEFGDKAA
ERRAYSNLGN AYIFLGEFET ASEYYKKTLL LARQLKDRAV EAQSCYSLGN TYTLLQDYEK
AIDYHLKHLA IAQELNDRIG EGRACWSLGN AYTALGNHDQ AMHFAEKHLE ISREVGDKSG
ELTARLNLSD LQMVLGLSYS TNNSIMSENT EIDSSLNGVR PKLGRRHSME NMELMKLTPE
KVQNWNSEIL AKQKPLIAKP SAKLLFVNRL KGKKYKTNSS TKVLQDASNS IDHRIPNSQR
KISADTIGDE GFFDLLSRFQ SNRMDDQRCC LQEKNCHTAS TTTSTPPKMM LKTSSVPVVS
PNTDEFLDLL ASSQSRRLDD QRASFSNLPG LRLTQNSQSV LSHLMTNDNK EADEDFFDIL
VKCQGSRLDD QRCAPPPATT KGPTVPDEDF FSLILRSQGK RMDEQRVLLQ RDQNRDTDFG
LKDFLQNNAL LEFKNSGKKS ADH*

Position of stopcodon in wt / mu CDS

2055 / 2052

Position (AA) of stopcodon in wt / mu AA sequence

685 / 684

Position of stopcodon in wt / mu cDNA

2364 / 2361

Position of start ATG in wt / mu cDNA

310 / 310

Last intron/exon boundary

2124

Theoretical NMD boundary in CDS

1764

Length of CDS

2055

Coding sequence (CDS) position

1567 / 1571

cDNA position

1876 / 1880

gDNA position

47194 / 47198

Chromosomal position

108922543 / 108922547

Speed

0.05 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

Back to summary table

MutationT@ster 2025

Variant:

1:108922543ACTT>A_4_ENST00000446797

Back to summary table

Prediction:

BenignPermalink

Summary:

Amino acid sequence changed
Homozygous in gnomAD
Protein features (might be) affected

Model: simple_aae
Tree vote: 63|37 (del | benign) ?
Automatic classification due to gnomAD,
tree vote conflicts with the automatic classification ?

Analysed issue

Analysis result

Variant

Chr1:108922544_108922546delCTT (GRCh38)

Gene symbol

GPSM2

Gene constraints

LOEUF: 0.86, LOF (oe): 0.60, misssense (oe): 0.80, synonymous (oe): 0.77 ? (gnomAD)

Ensembl transcript ID

ENST00000446797.2

Genbank transcript ID

UniProt / AlphaMissense peptide

GPSM2_HUMAN | AlphaMissense: transcript, gene

Variant type

Deletion

Gene region

CDS

DNA changes

c.1568_1570delCTT
g.47195_47197delCTT

AA changes

deletion of 1 or 2 AA

AAE:	S524-	?
Score:	-

Frameshift

No

Length of protein

Deletion of 1 or 2 AA

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs35029887
gnomAD	homozygous (-/-)	heterozygous	allele carriers
	>32000	>32000	>32000

Protein conservation

Species	Match	AA	Alignment
Human		524	E	K	N	C	H	T	A	S	T	T	T	S	S	T	P	P	K	M	M	L	K	T	S	S
mutated	not conserved	524	E	K	N	C	H	T	A	S	T	T	T	-	S	T	P	P	K	M	M	L	K	T	S
Ptroglodytes	no homologue
Mmulatta	no homologue
Fcatus	no homologue
Mmusculus	no homologue
Ggallus	no homologue
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	no homologue

Protein features

Start (aa)	End (aa)	Feature	Details
1	684	CHAIN		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.051	0.004
	1.779	0.007
	-0.709	0
	-0.613	0
(flanking)	3.525	0.07

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

1

Strand

1

Original gDNA sequence snippet

CCATACAGCTTCAACAACAACTTCTTCCACTCCCCCTAAAATG

Altered gDNA sequence snippet

CCATACAGCTTCAACAACAACTTCCACTCCCCCTAAAATG

Original cDNA sequence snippet

CCATACAGCTTCAACAACAACTTCTTCCACTCCCCCTAAAATG

Altered cDNA sequence snippet

CCATACAGCTTCAACAACAACTTCCACTCCCCCTAAAATG

Wildtype AA sequence

MEENLISMRE DHSFHVRYRM EASCLELALE GERLCKSGDC RAGVSFFEAA VQVGTEDLKT
LSAIYSQLGN AYFYLHDYAK ALEYHHHDLT LARTIGDQLG EAKASGNLGN TLKVLGNFDE
AIVCCQRHLD ISRELNDKVG EARALYNLGN VYHAKGKSFG CPGPQDVGEF PEEVRDALQA
AVDFYEENLS LVTALGDRAA QGRAFGNLGN THYLLGNFRD AVIAHEQRLL IAKEFGDKAA
ERRAYSNLGN AYIFLGEFET ASEYYKKTLL LARQLKDRAV EAQSCYSLGN TYTLLQDYEK
AIDYHLKHLA IAQELNDRIG EGRACWSLGN AYTALGNHDQ AMHFAEKHLE ISREVGDKSG
ELTARLNLSD LQMVLGLSYS TNNSIMSENT EIDSSLNGVR PKLGRRHSME NMELMKLTPE
KVQNWNSEIL AKQKPLIAKP SAKLLFVNRL KGKKYKTNSS TKVLQDASNS IDHRIPNSQR
KISADTIGDE GFFDLLSRFQ SNRMDDQRCC LQEKNCHTAS TTTSSTPPKM MLKTSSVPVV
SPNTDEFLDL LASSQSRRLD DQRASFSNLP GLRLTQNSQS VLSHLMTNDN KEADEDFFDI
LVKCQGSRLD DQRCAPPPAT TKGPTVPDED FFSLILRSQG KRMDEQRVLL QRDQNRDTDF
GLKDFLQNNA LLEFKNSGKK SADH*

Mutated AA sequence

MEENLISMRE DHSFHVRYRM EASCLELALE GERLCKSGDC RAGVSFFEAA VQVGTEDLKT
LSAIYSQLGN AYFYLHDYAK ALEYHHHDLT LARTIGDQLG EAKASGNLGN TLKVLGNFDE
AIVCCQRHLD ISRELNDKVG EARALYNLGN VYHAKGKSFG CPGPQDVGEF PEEVRDALQA
AVDFYEENLS LVTALGDRAA QGRAFGNLGN THYLLGNFRD AVIAHEQRLL IAKEFGDKAA
ERRAYSNLGN AYIFLGEFET ASEYYKKTLL LARQLKDRAV EAQSCYSLGN TYTLLQDYEK
AIDYHLKHLA IAQELNDRIG EGRACWSLGN AYTALGNHDQ AMHFAEKHLE ISREVGDKSG
ELTARLNLSD LQMVLGLSYS TNNSIMSENT EIDSSLNGVR PKLGRRHSME NMELMKLTPE
KVQNWNSEIL AKQKPLIAKP SAKLLFVNRL KGKKYKTNSS TKVLQDASNS IDHRIPNSQR
KISADTIGDE GFFDLLSRFQ SNRMDDQRCC LQEKNCHTAS TTTSTPPKMM LKTSSVPVVS
PNTDEFLDLL ASSQSRRLDD QRASFSNLPG LRLTQNSQSV LSHLMTNDNK EADEDFFDIL
VKCQGSRLDD QRCAPPPATT KGPTVPDEDF FSLILRSQGK RMDEQRVLLQ RDQNRDTDFG
LKDFLQNNAL LEFKNSGKKS ADH*

Position of stopcodon in wt / mu CDS

2055 / 2052

Position (AA) of stopcodon in wt / mu AA sequence

685 / 684

Position of stopcodon in wt / mu cDNA

2757 / 2754

Position of start ATG in wt / mu cDNA

703 / 703

Last intron/exon boundary

2517

Theoretical NMD boundary in CDS

1764

Length of CDS

2055

Coding sequence (CDS) position

1567 / 1571

cDNA position

2269 / 2273

gDNA position

47194 / 47198

Chromosomal position

108922543 / 108922547

Speed

0.05 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

Back to summary table

MutationT@ster 2025

Variant:

1:108922543ACTT>A_5_ENST00000675087

Back to summary table

Prediction:

BenignPermalink

Summary:

Amino acid sequence changed
Homozygous in gnomAD

Model: simple_aae
Tree vote: 63|37 (del | benign) ?
Automatic classification due to gnomAD,
tree vote conflicts with the automatic classification ?

Analysed issue

Analysis result

Variant

Chr1:108922544_108922546delCTT (GRCh38)

Gene symbol

GPSM2

Gene constraints

LOEUF: 0.86, LOF (oe): 0.60, misssense (oe): 0.80, synonymous (oe): 0.77 ? (gnomAD)

Ensembl transcript ID

ENST00000675087.1

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Deletion

Gene region

CDS

DNA changes

c.1619_1621delCTT
g.47195_47197delCTT

AA changes

deletion of 1 or 2 AA

AAE:	S541-	?
Score:	-

Frameshift

No

Length of protein

Deletion of 1 or 2 AA

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs35029887
gnomAD	homozygous (-/-)	heterozygous	allele carriers
	>32000	>32000	>32000

Protein conservation

Species	Match	AA	Alignment
Human		541	E	K	N	C	H	T	A	S	T	T	T	S	S	T	P	P	K	M	M	L	K	T	S	S
mutated	not conserved	541												-	S	T	P	P	K	M	M	L	K	T	S
Ptroglodytes	no homologue
Mmulatta	no homologue
Fcatus	no homologue
Mmusculus	no homologue
Ggallus	no homologue
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	no homologue

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.051	0.004
	1.779	0.007
	-0.709	0
	-0.613	0
(flanking)	3.525	0.07

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

1

Strand

1

Original gDNA sequence snippet

CCATACAGCTTCAACAACAACTTCTTCCACTCCCCCTAAAATG

Altered gDNA sequence snippet

CCATACAGCTTCAACAACAACTTCCACTCCCCCTAAAATG

Original cDNA sequence snippet

CCATACAGCTTCAACAACAACTTCTTCCACTCCCCCTAAAATG

Altered cDNA sequence snippet

CCATACAGCTTCAACAACAACTTCCACTCCCCCTAAAATG

Wildtype AA sequence

MFVTEMGVSL YCPGKSQTPG LKQSSCLSLQ SSRNYRMEAS CLELALEGER LCKSGDCRAG
VSFFEAAVQV GTEDLKTLSA IYSQLGNAYF YLHDYAKALE YHHHDLTLAR TIGDQLGEAK
ASGNLGNTLK VLGNFDEAIV CCQRHLDISR ELNDKVGEAR ALYNLGNVYH AKGKSFGCPG
PQDVGEFPEE VRDALQAAVD FYEENLSLVT ALGDRAAQGR AFGNLGNTHY LLGNFRDAVI
AHEQRLLIAK EFGDKAAERR AYSNLGNAYI FLGEFETASE YYKKTLLLAR QLKDRAVEAQ
SCYSLGNTYT LLQDYEKAID YHLKHLAIAQ ELNDRIGEGR ACWSLGNAYT ALGNHDQAMH
FAEKHLEISR EVGDKSGELT ARLNLSDLQM VLGLSYSTNN SIMSENTEID SSLNGVRPKL
GRRHSMENME LMKLTPEKVQ NWNSEILAKQ KPLIAKPSAK LLFVNRLKGK KYKTNSSTKV
LQDASNSIDH RIPNSQRKIS ADTIGDEGFF DLLSRFQSNR MDDQRCCLQE KNCHTASTTT
SSTPPKMMLK TSSVPVVSPN TDEFLDLLAS SQSRRLDDQR ASFSNLPGLR LTQNSQSVLS
HLMTNDNKEA DEDFFDILVK CQGSRLDDQR CAPPPATTKG PTVPDEDFFS LILRSQGKRM
DEQRVLLQRD QNRDTDFGLK DFLQNNALLE FKNSGKKSAD H*

Mutated AA sequence

MFVTEMGVSL YCPGKSQTPG LKQSSCLSLQ SSRNYRMEAS CLELALEGER LCKSGDCRAG
VSFFEAAVQV GTEDLKTLSA IYSQLGNAYF YLHDYAKALE YHHHDLTLAR TIGDQLGEAK
ASGNLGNTLK VLGNFDEAIV CCQRHLDISR ELNDKVGEAR ALYNLGNVYH AKGKSFGCPG
PQDVGEFPEE VRDALQAAVD FYEENLSLVT ALGDRAAQGR AFGNLGNTHY LLGNFRDAVI
AHEQRLLIAK EFGDKAAERR AYSNLGNAYI FLGEFETASE YYKKTLLLAR QLKDRAVEAQ
SCYSLGNTYT LLQDYEKAID YHLKHLAIAQ ELNDRIGEGR ACWSLGNAYT ALGNHDQAMH
FAEKHLEISR EVGDKSGELT ARLNLSDLQM VLGLSYSTNN SIMSENTEID SSLNGVRPKL
GRRHSMENME LMKLTPEKVQ NWNSEILAKQ KPLIAKPSAK LLFVNRLKGK KYKTNSSTKV
LQDASNSIDH RIPNSQRKIS ADTIGDEGFF DLLSRFQSNR MDDQRCCLQE KNCHTASTTT
STPPKMMLKT SSVPVVSPNT DEFLDLLASS QSRRLDDQRA SFSNLPGLRL TQNSQSVLSH
LMTNDNKEAD EDFFDILVKC QGSRLDDQRC APPPATTKGP TVPDEDFFSL ILRSQGKRMD
EQRVLLQRDQ NRDTDFGLKD FLQNNALLEF KNSGKKSADH *

Position of stopcodon in wt / mu CDS

2106 / 2103

Position (AA) of stopcodon in wt / mu AA sequence

702 / 701

Position of stopcodon in wt / mu cDNA

2385 / 2382

Position of start ATG in wt / mu cDNA

280 / 280

Last intron/exon boundary

2145

Theoretical NMD boundary in CDS

1815

Length of CDS

2106

Coding sequence (CDS) position

1618 / 1622

cDNA position

1897 / 1901

gDNA position

47194 / 47198

Chromosomal position

108922543 / 108922547

Speed

0.05 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

Back to summary table

MutationT@ster 2025

Variant:

1:108922543ACTT>A_6_ENST00000676184

Back to summary table

Prediction:

BenignPermalink

Summary:

Amino acid sequence changed
Homozygous in gnomAD
Protein features (might be) affected

Model: simple_aae
Tree vote: 63|37 (del | benign) ?
Automatic classification due to gnomAD,
tree vote conflicts with the automatic classification ?

Analysed issue

Analysis result

Variant

Chr1:108922544_108922546delCTT (GRCh38)

Gene symbol

GPSM2

Gene constraints

LOEUF: 0.86, LOF (oe): 0.60, misssense (oe): 0.80, synonymous (oe): 0.77 ? (gnomAD)

Ensembl transcript ID

ENST00000676184.1

Genbank transcript ID

UniProt / AlphaMissense peptide

GPSM2_HUMAN | AlphaMissense: transcript, gene

Variant type

Deletion

Gene region

CDS

DNA changes

c.1568_1570delCTT
g.47195_47197delCTT

AA changes

deletion of 1 or 2 AA

AAE:	S524-	?
Score:	-

Frameshift

No

Length of protein

Deletion of 1 or 2 AA

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs35029887
gnomAD	homozygous (-/-)	heterozygous	allele carriers
	>32000	>32000	>32000

Protein conservation

Species	Match	AA	Alignment
Human		524	E	K	N	C	H	T	A	S	T	T	T	S	S	T	P	P	K	M	M	L	K	T	S	S
mutated	not conserved	524	E	K	N	C	H	T	A	S	T	T	T	-	S	T	P	P	K	M	M	L	K	T	S
Ptroglodytes	no homologue
Mmulatta	no homologue
Fcatus	no homologue
Mmusculus	no homologue
Ggallus	no homologue
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	no homologue

Protein features

Start (aa)	End (aa)	Feature	Details
1	684	CHAIN		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.051	0.004
	1.779	0.007
	-0.709	0
	-0.613	0
(flanking)	3.525	0.07

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

1

Strand

1

Original gDNA sequence snippet

CCATACAGCTTCAACAACAACTTCTTCCACTCCCCCTAAAATG

Altered gDNA sequence snippet

CCATACAGCTTCAACAACAACTTCCACTCCCCCTAAAATG

Original cDNA sequence snippet

CCATACAGCTTCAACAACAACTTCTTCCACTCCCCCTAAAATG

Altered cDNA sequence snippet

CCATACAGCTTCAACAACAACTTCCACTCCCCCTAAAATG

Wildtype AA sequence

MEENLISMRE DHSFHVRYRM EASCLELALE GERLCKSGDC RAGVSFFEAA VQVGTEDLKT
LSAIYSQLGN AYFYLHDYAK ALEYHHHDLT LARTIGDQLG EAKASGNLGN TLKVLGNFDE
AIVCCQRHLD ISRELNDKVG EARALYNLGN VYHAKGKSFG CPGPQDVGEF PEEVRDALQA
AVDFYEENLS LVTALGDRAA QGRAFGNLGN THYLLGNFRD AVIAHEQRLL IAKEFGDKAA
ERRAYSNLGN AYIFLGEFET ASEYYKKTLL LARQLKDRAV EAQSCYSLGN TYTLLQDYEK
AIDYHLKHLA IAQELNDRIG EGRACWSLGN AYTALGNHDQ AMHFAEKHLE ISREVGDKSG
ELTARLNLSD LQMVLGLSYS TNNSIMSENT EIDSSLNGVR PKLGRRHSME NMELMKLTPE
KVQNWNSEIL AKQKPLIAKP SAKLLFVNRL KGKKYKTNSS TKVLQDASNS IDHRIPNSQR
KISADTIGDE GFFDLLSRFQ SNRMDDQRCC LQEKNCHTAS TTTSSTPPKM MLKTSSVPVV
SPNTDEFLDL LASSQSRRLD DQRASFSNLP GLRLTQNSQS VLSHLMTNDN KEADEDFFDI
LVKCQGSRLD DQRCAPPPAT TKGPTVPDED FFSLILRSQG KRMDEQRVLL QRDQNRDTDF
GLKDFLQNNA LLEFKNSGKK SADH*

Mutated AA sequence

MEENLISMRE DHSFHVRYRM EASCLELALE GERLCKSGDC RAGVSFFEAA VQVGTEDLKT
LSAIYSQLGN AYFYLHDYAK ALEYHHHDLT LARTIGDQLG EAKASGNLGN TLKVLGNFDE
AIVCCQRHLD ISRELNDKVG EARALYNLGN VYHAKGKSFG CPGPQDVGEF PEEVRDALQA
AVDFYEENLS LVTALGDRAA QGRAFGNLGN THYLLGNFRD AVIAHEQRLL IAKEFGDKAA
ERRAYSNLGN AYIFLGEFET ASEYYKKTLL LARQLKDRAV EAQSCYSLGN TYTLLQDYEK
AIDYHLKHLA IAQELNDRIG EGRACWSLGN AYTALGNHDQ AMHFAEKHLE ISREVGDKSG
ELTARLNLSD LQMVLGLSYS TNNSIMSENT EIDSSLNGVR PKLGRRHSME NMELMKLTPE
KVQNWNSEIL AKQKPLIAKP SAKLLFVNRL KGKKYKTNSS TKVLQDASNS IDHRIPNSQR
KISADTIGDE GFFDLLSRFQ SNRMDDQRCC LQEKNCHTAS TTTSTPPKMM LKTSSVPVVS
PNTDEFLDLL ASSQSRRLDD QRASFSNLPG LRLTQNSQSV LSHLMTNDNK EADEDFFDIL
VKCQGSRLDD QRCAPPPATT KGPTVPDEDF FSLILRSQGK RMDEQRVLLQ RDQNRDTDFG
LKDFLQNNAL LEFKNSGKKS ADH*

Position of stopcodon in wt / mu CDS

2055 / 2052

Position (AA) of stopcodon in wt / mu AA sequence

685 / 684

Position of stopcodon in wt / mu cDNA

2304 / 2301

Position of start ATG in wt / mu cDNA

250 / 250

Last intron/exon boundary

2064

Theoretical NMD boundary in CDS

1764

Length of CDS

2055

Coding sequence (CDS) position

1567 / 1571

cDNA position

1816 / 1820

gDNA position

47194 / 47198

Chromosomal position

108922543 / 108922547

Speed

0.05 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

Back to summary table

MutationT@ster 2025

Variant:

1:108922543ACTT>A_9_ENST00000674914

Back to summary table

Prediction:

BenignPermalink

Summary:

Amino acid sequence changed
Homozygous in gnomAD

Model: simple_aae
Tree vote: 63|37 (del | benign) ?
Automatic classification due to gnomAD,
tree vote conflicts with the automatic classification ?

Analysed issue

Analysis result

Variant

Chr1:108922544_108922546delCTT (GRCh38)

Gene symbol

GPSM2

Gene constraints

LOEUF: 0.86, LOF (oe): 0.60, misssense (oe): 0.80, synonymous (oe): 0.77 ? (gnomAD)

Ensembl transcript ID

ENST00000674914.1

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Deletion

Gene region

CDS

DNA changes

c.1619_1621delCTT
g.47195_47197delCTT

AA changes

deletion of 1 or 2 AA

AAE:	S541-	?
Score:	-

Frameshift

No

Length of protein

Deletion of 1 or 2 AA

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs35029887
gnomAD	homozygous (-/-)	heterozygous	allele carriers
	>32000	>32000	>32000

Protein conservation

Species	Match	AA	Alignment
Human		541	E	K	N	C	H	T	A	S	T	T	T	S	S	T	P	P	K	M	M	L	K	T	S	S
mutated	not conserved	541												-	S	T	P	P	K	M	M	L	K	T	S
Ptroglodytes	no homologue
Mmulatta	no homologue
Fcatus	no homologue
Mmusculus	no homologue
Ggallus	no homologue
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	no homologue

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.051	0.004
	1.779	0.007
	-0.709	0
	-0.613	0
(flanking)	3.525	0.07

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

1

Strand

1

Original gDNA sequence snippet

CCATACAGCTTCAACAACAACTTCTTCCACTCCCCCTAAAATG

Altered gDNA sequence snippet

CCATACAGCTTCAACAACAACTTCCACTCCCCCTAAAATG

Original cDNA sequence snippet

CCATACAGCTTCAACAACAACTTCTTCCACTCCCCCTAAAATG

Altered cDNA sequence snippet

CCATACAGCTTCAACAACAACTTCCACTCCCCCTAAAATG

Wildtype AA sequence

MFVTEMGVSL YCPGKSQTPG LKQSSCLSLQ SSRNYRMEAS CLELALEGER LCKSGDCRAG
VSFFEAAVQV GTEDLKTLSA IYSQLGNAYF YLHDYAKALE YHHHDLTLAR TIGDQLGEAK
ASGNLGNTLK VLGNFDEAIV CCQRHLDISR ELNDKVGEAR ALYNLGNVYH AKGKSFGCPG
PQDVGEFPEE VRDALQAAVD FYEENLSLVT ALGDRAAQGR AFGNLGNTHY LLGNFRDAVI
AHEQRLLIAK EFGDKAAERR AYSNLGNAYI FLGEFETASE YYKKTLLLAR QLKDRAVEAQ
SCYSLGNTYT LLQDYEKAID YHLKHLAIAQ ELNDRIGEGR ACWSLGNAYT ALGNHDQAMH
FAEKHLEISR EVGDKSGELT ARLNLSDLQM VLGLSYSTNN SIMSENTEID SSLNGVRPKL
GRRHSMENME LMKLTPEKVQ NWNSEILAKQ KPLIAKPSAK LLFVNRLKGK KYKTNSSTKV
LQDASNSIDH RIPNSQRKIS ADTIGDEGFF DLLSRFQSNR MDDQRCCLQE KNCHTASTTT
SSTPPKMMLK TSSVPVVSPN TDEFLDLLAS SQSRRLDDQR ASFSNLPGLR LTQNSQSVLS
HLMTNDNKEA DEDFFDILVK CQGSRLDDQR CAPPPATTKG PTVPDEDFFS LILRSQGKRM
DEQRVLLQRD QNRDTDFGLK DFLQNNALLE FKNSGKKSAD H*

Mutated AA sequence

MFVTEMGVSL YCPGKSQTPG LKQSSCLSLQ SSRNYRMEAS CLELALEGER LCKSGDCRAG
VSFFEAAVQV GTEDLKTLSA IYSQLGNAYF YLHDYAKALE YHHHDLTLAR TIGDQLGEAK
ASGNLGNTLK VLGNFDEAIV CCQRHLDISR ELNDKVGEAR ALYNLGNVYH AKGKSFGCPG
PQDVGEFPEE VRDALQAAVD FYEENLSLVT ALGDRAAQGR AFGNLGNTHY LLGNFRDAVI
AHEQRLLIAK EFGDKAAERR AYSNLGNAYI FLGEFETASE YYKKTLLLAR QLKDRAVEAQ
SCYSLGNTYT LLQDYEKAID YHLKHLAIAQ ELNDRIGEGR ACWSLGNAYT ALGNHDQAMH
FAEKHLEISR EVGDKSGELT ARLNLSDLQM VLGLSYSTNN SIMSENTEID SSLNGVRPKL
GRRHSMENME LMKLTPEKVQ NWNSEILAKQ KPLIAKPSAK LLFVNRLKGK KYKTNSSTKV
LQDASNSIDH RIPNSQRKIS ADTIGDEGFF DLLSRFQSNR MDDQRCCLQE KNCHTASTTT
STPPKMMLKT SSVPVVSPNT DEFLDLLASS QSRRLDDQRA SFSNLPGLRL TQNSQSVLSH
LMTNDNKEAD EDFFDILVKC QGSRLDDQRC APPPATTKGP TVPDEDFFSL ILRSQGKRMD
EQRVLLQRDQ NRDTDFGLKD FLQNNALLEF KNSGKKSADH *

Position of stopcodon in wt / mu CDS

2106 / 2103

Position (AA) of stopcodon in wt / mu AA sequence

702 / 701

Position of stopcodon in wt / mu cDNA

2401 / 2398

Position of start ATG in wt / mu cDNA

296 / 296

Last intron/exon boundary

2161

Theoretical NMD boundary in CDS

1815

Length of CDS

2106

Coding sequence (CDS) position

1618 / 1622

cDNA position

1913 / 1917

gDNA position

47194 / 47198

Chromosomal position

108922543 / 108922547

Speed

0.05 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

Back to summary table

MutationT@ster 2025

Variant:

1:108922543ACTT>A_10_ENST00000264126

Back to summary table

Prediction:

BenignPermalink

Summary:

Amino acid sequence changed
Homozygous in gnomAD
Protein features (might be) affected

Model: simple_aae
Tree vote: 63|37 (del | benign) ?
Automatic classification due to gnomAD,
tree vote conflicts with the automatic classification ?

Analysed issue

Analysis result

Variant

Chr1:108922544_108922546delCTT (GRCh38)

Gene symbol

GPSM2

Gene constraints

LOEUF: 0.86, LOF (oe): 0.60, misssense (oe): 0.80, synonymous (oe): 0.77 ? (gnomAD)

Ensembl transcript ID

ENST00000264126.9

Genbank transcript ID

NM_013296 (exact from MANE), NM_001321038 (by similarity)

UniProt / AlphaMissense peptide

GPSM2_HUMAN | AlphaMissense: transcript, gene

Variant type

Deletion

Gene region

CDS

DNA changes

c.1568_1570delCTT
g.47195_47197delCTT

AA changes

deletion of 1 or 2 AA

AAE:	S524-	?
Score:	-

Frameshift

No

Length of protein

Deletion of 1 or 2 AA

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs35029887
gnomAD	homozygous (-/-)	heterozygous	allele carriers
	>32000	>32000	>32000

Protein conservation

Species	Match	AA	Alignment
Human		524	E	K	N	C	H	T	A	S	T	T	T	S	S	T	P	P	K	M	M	L	K	T	S	S
mutated	not conserved	524	E	K	N	C	H	T	A	S	T	T	T	-	S	T	P	P	K	M	M	L	K	T	S
Ptroglodytes	all identical	524	E	K	N	C	H	T	A	S	T	T	P	S	S	T	P	P	K	M	M	L	K	T	P
Mmulatta	all identical	525	E	K	N	S	H	T	V	S	T	T	T	S	S	T	P	P	K	M	M	L	K	T	P
Fcatus	all identical	610	E	Q	S	C	G	T	A	S	A	A	A	S	S	T	P	P	R	V	M	M	K	A	P
Mmusculus	all conserved	525	-	G	N	C	R	T	T	S	T	A	A	A	S	A	T	P	K	L	M	-	K	A	P
Ggallus	no homologue
Trubripes	all identical	529	D	S	P	S	R	L	P	P	P	S	P	S	S	T	P	PVAE	R
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	no homologue

Protein features

Start (aa)	End (aa)	Feature	Details
1	684	CHAIN		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.051	0.004
	1.779	0.007
	-0.709	0
	-0.613	0
(flanking)	3.525	0.07

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

1

Strand

1

Original gDNA sequence snippet

CCATACAGCTTCAACAACAACTTCTTCCACTCCCCCTAAAATG

Altered gDNA sequence snippet

CCATACAGCTTCAACAACAACTTCCACTCCCCCTAAAATG

Original cDNA sequence snippet

CCATACAGCTTCAACAACAACTTCTTCCACTCCCCCTAAAATG

Altered cDNA sequence snippet

CCATACAGCTTCAACAACAACTTCCACTCCCCCTAAAATG

Wildtype AA sequence

MEENLISMRE DHSFHVRYRM EASCLELALE GERLCKSGDC RAGVSFFEAA VQVGTEDLKT
LSAIYSQLGN AYFYLHDYAK ALEYHHHDLT LARTIGDQLG EAKASGNLGN TLKVLGNFDE
AIVCCQRHLD ISRELNDKVG EARALYNLGN VYHAKGKSFG CPGPQDVGEF PEEVRDALQA
AVDFYEENLS LVTALGDRAA QGRAFGNLGN THYLLGNFRD AVIAHEQRLL IAKEFGDKAA
ERRAYSNLGN AYIFLGEFET ASEYYKKTLL LARQLKDRAV EAQSCYSLGN TYTLLQDYEK
AIDYHLKHLA IAQELNDRIG EGRACWSLGN AYTALGNHDQ AMHFAEKHLE ISREVGDKSG
ELTARLNLSD LQMVLGLSYS TNNSIMSENT EIDSSLNGVR PKLGRRHSME NMELMKLTPE
KVQNWNSEIL AKQKPLIAKP SAKLLFVNRL KGKKYKTNSS TKVLQDASNS IDHRIPNSQR
KISADTIGDE GFFDLLSRFQ SNRMDDQRCC LQEKNCHTAS TTTSSTPPKM MLKTSSVPVV
SPNTDEFLDL LASSQSRRLD DQRASFSNLP GLRLTQNSQS VLSHLMTNDN KEADEDFFDI
LVKCQGSRLD DQRCAPPPAT TKGPTVPDED FFSLILRSQG KRMDEQRVLL QRDQNRDTDF
GLKDFLQNNA LLEFKNSGKK SADH*

Mutated AA sequence

MEENLISMRE DHSFHVRYRM EASCLELALE GERLCKSGDC RAGVSFFEAA VQVGTEDLKT
LSAIYSQLGN AYFYLHDYAK ALEYHHHDLT LARTIGDQLG EAKASGNLGN TLKVLGNFDE
AIVCCQRHLD ISRELNDKVG EARALYNLGN VYHAKGKSFG CPGPQDVGEF PEEVRDALQA
AVDFYEENLS LVTALGDRAA QGRAFGNLGN THYLLGNFRD AVIAHEQRLL IAKEFGDKAA
ERRAYSNLGN AYIFLGEFET ASEYYKKTLL LARQLKDRAV EAQSCYSLGN TYTLLQDYEK
AIDYHLKHLA IAQELNDRIG EGRACWSLGN AYTALGNHDQ AMHFAEKHLE ISREVGDKSG
ELTARLNLSD LQMVLGLSYS TNNSIMSENT EIDSSLNGVR PKLGRRHSME NMELMKLTPE
KVQNWNSEIL AKQKPLIAKP SAKLLFVNRL KGKKYKTNSS TKVLQDASNS IDHRIPNSQR
KISADTIGDE GFFDLLSRFQ SNRMDDQRCC LQEKNCHTAS TTTSTPPKMM LKTSSVPVVS
PNTDEFLDLL ASSQSRRLDD QRASFSNLPG LRLTQNSQSV LSHLMTNDNK EADEDFFDIL
VKCQGSRLDD QRCAPPPATT KGPTVPDEDF FSLILRSQGK RMDEQRVLLQ RDQNRDTDFG
LKDFLQNNAL LEFKNSGKKS ADH*

Position of stopcodon in wt / mu CDS

2055 / 2052

Position (AA) of stopcodon in wt / mu AA sequence

685 / 684

Position of stopcodon in wt / mu cDNA

2547 / 2544

Position of start ATG in wt / mu cDNA

493 / 493

Last intron/exon boundary

2307

Theoretical NMD boundary in CDS

1764

Length of CDS

2055

Coding sequence (CDS) position

1567 / 1571

cDNA position

2059 / 2063

gDNA position

47194 / 47198

Chromosomal position

108922543 / 108922547

Speed

0.06 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

Back to summary table

MutationT@ster 2025

Variant:

1:108922543ACTT>A_11_ENST00000642355

Back to summary table

Prediction:

BenignPermalink

Summary:

Amino acid sequence changed
Homozygous in gnomAD
Protein features (might be) affected

Model: simple_aae
Tree vote: 63|37 (del | benign) ?
Automatic classification due to gnomAD,
tree vote conflicts with the automatic classification ?

Analysed issue

Analysis result

Variant

Chr1:108922544_108922546delCTT (GRCh38)

Gene symbol

GPSM2

Gene constraints

LOEUF: 0.86, LOF (oe): 0.60, misssense (oe): 0.80, synonymous (oe): 0.77 ? (gnomAD)

Ensembl transcript ID

ENST00000642355.1

Genbank transcript ID

NM_001321039 (by similarity)

UniProt / AlphaMissense peptide

GPSM2_HUMAN | AlphaMissense: transcript, gene

Variant type

Deletion

Gene region

CDS

DNA changes

c.1568_1570delCTT
g.47195_47197delCTT

AA changes

deletion of 1 or 2 AA

AAE:	S524-	?
Score:	-

Frameshift

No

Length of protein

Deletion of 1 or 2 AA

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs35029887
gnomAD	homozygous (-/-)	heterozygous	allele carriers
	>32000	>32000	>32000

Protein conservation

Species	Match	AA	Alignment
Human		524	E	K	N	C	H	T	A	S	T	T	T	S	S	T	P	P	K	M	M	L	K	T	S	S
mutated	not conserved	524	E	K	N	C	H	T	A	S	T	T	T	-	S	T	P	P	K	M	M	L	K	T	S
Ptroglodytes	no homologue
Mmulatta	no homologue
Fcatus	no homologue
Mmusculus	no homologue
Ggallus	no homologue
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	no homologue

Protein features

Start (aa)	End (aa)	Feature	Details
1	684	CHAIN		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.051	0.004
	1.779	0.007
	-0.709	0
	-0.613	0
(flanking)	3.525	0.07

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

1

Strand

1

Original gDNA sequence snippet

CCATACAGCTTCAACAACAACTTCTTCCACTCCCCCTAAAATG

Altered gDNA sequence snippet

CCATACAGCTTCAACAACAACTTCCACTCCCCCTAAAATG

Original cDNA sequence snippet

CCATACAGCTTCAACAACAACTTCTTCCACTCCCCCTAAAATG

Altered cDNA sequence snippet

CCATACAGCTTCAACAACAACTTCCACTCCCCCTAAAATG

Wildtype AA sequence

MEENLISMRE DHSFHVRYRM EASCLELALE GERLCKSGDC RAGVSFFEAA VQVGTEDLKT
LSAIYSQLGN AYFYLHDYAK ALEYHHHDLT LARTIGDQLG EAKASGNLGN TLKVLGNFDE
AIVCCQRHLD ISRELNDKVG EARALYNLGN VYHAKGKSFG CPGPQDVGEF PEEVRDALQA
AVDFYEENLS LVTALGDRAA QGRAFGNLGN THYLLGNFRD AVIAHEQRLL IAKEFGDKAA
ERRAYSNLGN AYIFLGEFET ASEYYKKTLL LARQLKDRAV EAQSCYSLGN TYTLLQDYEK
AIDYHLKHLA IAQELNDRIG EGRACWSLGN AYTALGNHDQ AMHFAEKHLE ISREVGDKSG
ELTARLNLSD LQMVLGLSYS TNNSIMSENT EIDSSLNGVR PKLGRRHSME NMELMKLTPE
KVQNWNSEIL AKQKPLIAKP SAKLLFVNRL KGKKYKTNSS TKVLQDASNS IDHRIPNSQR
KISADTIGDE GFFDLLSRFQ SNRMDDQRCC LQEKNCHTAS TTTSSTPPKM MLKTSSVPVV
SPNTDEFLDL LASSQSRRLD DQRASFSNLP GLRLTQNSQS VLSHLMTNDN KEADEDFFDI
LVKCQGSRLD DQRCAPPPAT TKGPTVPDED FFSLILRSQG KRMDEQRVLL QRDQNRDTDF
GLKDFLQNNA LLEFKNSGKK SADH*

Mutated AA sequence

MEENLISMRE DHSFHVRYRM EASCLELALE GERLCKSGDC RAGVSFFEAA VQVGTEDLKT
LSAIYSQLGN AYFYLHDYAK ALEYHHHDLT LARTIGDQLG EAKASGNLGN TLKVLGNFDE
AIVCCQRHLD ISRELNDKVG EARALYNLGN VYHAKGKSFG CPGPQDVGEF PEEVRDALQA
AVDFYEENLS LVTALGDRAA QGRAFGNLGN THYLLGNFRD AVIAHEQRLL IAKEFGDKAA
ERRAYSNLGN AYIFLGEFET ASEYYKKTLL LARQLKDRAV EAQSCYSLGN TYTLLQDYEK
AIDYHLKHLA IAQELNDRIG EGRACWSLGN AYTALGNHDQ AMHFAEKHLE ISREVGDKSG
ELTARLNLSD LQMVLGLSYS TNNSIMSENT EIDSSLNGVR PKLGRRHSME NMELMKLTPE
KVQNWNSEIL AKQKPLIAKP SAKLLFVNRL KGKKYKTNSS TKVLQDASNS IDHRIPNSQR
KISADTIGDE GFFDLLSRFQ SNRMDDQRCC LQEKNCHTAS TTTSTPPKMM LKTSSVPVVS
PNTDEFLDLL ASSQSRRLDD QRASFSNLPG LRLTQNSQSV LSHLMTNDNK EADEDFFDIL
VKCQGSRLDD QRCAPPPATT KGPTVPDEDF FSLILRSQGK RMDEQRVLLQ RDQNRDTDFG
LKDFLQNNAL LEFKNSGKKS ADH*

Position of stopcodon in wt / mu CDS

2055 / 2052

Position (AA) of stopcodon in wt / mu AA sequence

685 / 684

Position of stopcodon in wt / mu cDNA

2551 / 2548

Position of start ATG in wt / mu cDNA

497 / 497

Last intron/exon boundary

2586

Theoretical NMD boundary in CDS

2039

Length of CDS

2055

Coding sequence (CDS) position

1567 / 1571

cDNA position

2063 / 2067

gDNA position

47194 / 47198

Chromosomal position

108922543 / 108922547

Speed

0.05 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

Back to summary table

MutationT@ster 2025

Variant:

1:108922543ACTT>A_7_ENST00000675086

Back to summary table

Prediction:

BenignPermalink

Summary:

Amino acid sequence changed
Homozygous in gnomAD

Model: simple_aae
Tree vote: 70|30 (del | benign) ?
Automatic classification due to gnomAD,
tree vote conflicts with the automatic classification ?

Analysed issue

Analysis result

Variant

Chr1:108922544_108922546delCTT (GRCh38)

Gene symbol

GPSM2

Gene constraints

LOEUF: 0.89, LOF (oe): 0.60, misssense (oe): 0.81, synonymous (oe): 0.79 ? (gnomAD)

Ensembl transcript ID

ENST00000675086.1

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Deletion

Gene region

CDS

DNA changes

c.1391_1393delCTT
g.47195_47197delCTT

AA changes

deletion of 1 or 2 AA

AAE:	S465-	?
Score:	-

Frameshift

No

Length of protein

Deletion of 1 or 2 AA

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs35029887
gnomAD	homozygous (-/-)	heterozygous	allele carriers
	>32000	>32000	>32000

Protein conservation

Species	Match	AA	Alignment
Human		465	E	K	N	C	H	T	A	S	T	T	T	S	S	T	P	P	K	M	M	L	K	T	S	S
mutated	not conserved	465	E	K	N	C	H	T	A	S	T	T	T	-	S	T	P	P	K	M	M	L	K	T	S
Ptroglodytes	no homologue
Mmulatta	no homologue
Fcatus	no homologue
Mmusculus	no homologue
Ggallus	no homologue
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	no homologue

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.051	0.004
	1.779	0.007
	-0.709	0
	-0.613	0
(flanking)	3.525	0.07

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

1

Strand

1

Original gDNA sequence snippet

CCATACAGCTTCAACAACAACTTCTTCCACTCCCCCTAAAATG

Altered gDNA sequence snippet

CCATACAGCTTCAACAACAACTTCCACTCCCCCTAAAATG

Original cDNA sequence snippet

CCATACAGCTTCAACAACAACTTCTTCCACTCCCCCTAAAATG

Altered cDNA sequence snippet

CCATACAGCTTCAACAACAACTTCCACTCCCCCTAAAATG

Wildtype AA sequence

MEENLISMRE DHSFHVRYRM EASCLELALE GERLCKSGDC RAGVSFFEAA VQVGTEDLKT
LSAIYSQLGN AYFYLHDYAK ALEYHHHDLT LARTIGDQLG EAKASGNLGN TLKVLGNFDE
AIVCCQRHLD ISRELNDKVG EARALYNLGN VYHAKGKSFG CPGPQDVGEF PEEVRDALQA
AVDFYEENLS LVTALGDRAA QGRAFGNLGN THYLLGNFRD AVIAHEQRLL IAKEFGDKAA
ERRAYSNLGN AYIFLGEFET ASEYYKKTLL LARQLKDRAV EAQSCYSLGN TYTLLQDYEK
AIDYHLKHLA IAQELNDRIG EGRACWSLGN AYTALGNHDQ AMHFAEKHLE ISREVGDKSG
ELTARLNLSD LQMVLGLSYS TNNSIMSENT EIDSSLNGVR PKLGRRHSME NMELMKLTPE
KKISADTIGD EGFFDLLSRF QSNRMDDQRC CLQEKNCHTA STTTSSTPPK MMLKTSSVPV
VSPNTDEFLD LLASSQSRRL DDQRASFSNL PGLRLTQNSQ SVLSHLMTND NKEADEDFFD
ILVKCQGSRL DDQRCAPPPA TTKGPTVPDE DFFSLILRSQ GKRMDEQRVL LQRDQNRDTD
FGLKDFLQNN ALLEFKNSGK KSADH*

Mutated AA sequence

MEENLISMRE DHSFHVRYRM EASCLELALE GERLCKSGDC RAGVSFFEAA VQVGTEDLKT
LSAIYSQLGN AYFYLHDYAK ALEYHHHDLT LARTIGDQLG EAKASGNLGN TLKVLGNFDE
AIVCCQRHLD ISRELNDKVG EARALYNLGN VYHAKGKSFG CPGPQDVGEF PEEVRDALQA
AVDFYEENLS LVTALGDRAA QGRAFGNLGN THYLLGNFRD AVIAHEQRLL IAKEFGDKAA
ERRAYSNLGN AYIFLGEFET ASEYYKKTLL LARQLKDRAV EAQSCYSLGN TYTLLQDYEK
AIDYHLKHLA IAQELNDRIG EGRACWSLGN AYTALGNHDQ AMHFAEKHLE ISREVGDKSG
ELTARLNLSD LQMVLGLSYS TNNSIMSENT EIDSSLNGVR PKLGRRHSME NMELMKLTPE
KKISADTIGD EGFFDLLSRF QSNRMDDQRC CLQEKNCHTA STTTSTPPKM MLKTSSVPVV
SPNTDEFLDL LASSQSRRLD DQRASFSNLP GLRLTQNSQS VLSHLMTNDN KEADEDFFDI
LVKCQGSRLD DQRCAPPPAT TKGPTVPDED FFSLILRSQG KRMDEQRVLL QRDQNRDTDF
GLKDFLQNNA LLEFKNSGKK SADH*

Position of stopcodon in wt / mu CDS

1878 / 1875

Position (AA) of stopcodon in wt / mu AA sequence

626 / 625

Position of stopcodon in wt / mu cDNA

2220 / 2217

Position of start ATG in wt / mu cDNA

343 / 343

Last intron/exon boundary

1980

Theoretical NMD boundary in CDS

1587

Length of CDS

1878

Coding sequence (CDS) position

1390 / 1394

cDNA position

1732 / 1736

gDNA position

47194 / 47198

Chromosomal position

108922543 / 108922547

Speed

0.05 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

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