MutationT @ ster 2025

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Frameshift
Known disease mutation: ClinVar ID 374899 (pathogenic)
NMD

Model: complex_aae
Tree vote: 10|0 (del | benign) ?
Automatic classification due to ClinVar

Analysed issue

Analysis result

Variant

Chr4:112646356_112646357insAT (GRCh38)

Gene symbol

Gene constraints

no data

Ensembl transcript ID

ENST00000694891.1

Genbank transcript ID

NM_001370979 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Insertion

Gene region

CDS

DNA changes

c.208_209insAT
g.9280_9281insAT

AA changes

S72Yfs*10

Frameshift

Yes

Length of protein

NMD

Pathogenic variant (ClinVar)

Microcephalic primordial dwarfism, Alazami type

pathogenic

Variant DBs

	Not in dbSNP
	Allele 'AT' was not found in gnomAD

Protein conservation

Species	Match	AA	Alignment
Human		72	I	E	K	S	R	D	G	Y	V	D	I	S	L	L	V	S	F	N	K	M	K	K	L	T
mutated	no alignment	n/a
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)	9.286	1
(flanking)	8.653	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

7

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

4

Strand

1

Original gDNA sequence snippet

TTCATTTTCTTTAGATGTTGATATATCACTACTTGTGTCT

Altered gDNA sequence snippet

TTCATTTTCTTTAGATGTTGATATATATCACTACTTGTGTCT

Original cDNA sequence snippet

ATCTAGAGATGGATATGTTGATATATCACTACTTGTGTCT

Altered cDNA sequence snippet

ATCTAGAGATGGATATGTTGATATATATCACTACTTGTGTCT

Wildtype AA sequence

METESGNQEK VMEEESTEKK KEVEKKKRSR VKQVLADIAK QVDFWFGDAN LHKDRFLREQ
IEKSRDGYVD ISLLVSFNKM KKLTTDGKLI ARALRSSAVV ELDLEGTRIR RKKPLGERPK
DEDERTVYVE LLPKNVNHSW IERVFGKCGN VVYISIPHYK STGDPKGFAF VEFETKEQAA
KAIEFLNNPP EEAPRKPGIF PKTVKNKPIP ALRVVEKKKK KKKKGRMKKE DNIQAKEENM
DTSNTSISKM KRSRPTSEGS DIESTEPQKQ CSKKKKKRDR VEASSLPEVR TGKRKRSSSE
DAESLAPRSK VKKIIQKDII KEASEASKEN RDIEISTEEE KDTGDLKDSS LLKTKRKHKK
KHKERHKMGE EVIPLRVLSK SEWMDLKKEY LALQKASMAS LKKTISQIKS ESEMETDSGV
PQNTGMKNEK TANREECRTQ EKVNATGPQF VSGVIVKIIS TEPLPGRKQV RDTLAAISEV
LYVDLLEGDT ECHARFKTPE DAQAVINAYT EINKKHCWKL EILSGDHEQR YWQKILVDRQ
AKLNQPREKK RGTEKLITKA EKIRLAKTQQ ASKHIRFSEY D*

Mutated AA sequence

METESGNQEK VMEEESTEKK KEVEKKKRSR VKQVLADIAK QVDFWFGDAN LHKDRFLREQ
IEKSRDGYVD IYHYLCLLTK *

Position of stopcodon in wt / mu CDS

1746 / 243

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

582 / 81

Position of stopcodon in wt / mu cDNA

1868 / 365

Position of start ATG in wt / mu cDNA

123 / 123

Last intron/exon boundary

1787

Theoretical NMD boundary in CDS

1614

Length of CDS

1746

Coding sequence (CDS) position

208 / 209

cDNA position

330 / 331

gDNA position

9280 / 9281

Chromosomal position

112646356 / 112646357

Speed

0.07 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

MutationT@ster 2025

Variant:

4:112646356G>GAT_2_ENST00000509061

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Frameshift
Known disease mutation: ClinVar ID 374899 (pathogenic)
NMD
Protein features (might be) affected

Model: complex_aae
Tree vote: 10|0 (del | benign) ?
Automatic classification due to ClinVar

Analysed issue

Analysis result

Variant

Chr4:112646356_112646357insAT (GRCh38)

Gene symbol

Gene constraints

LOEUF: 1.13, LOF (oe): 0.85, misssense (oe): 1.12, synonymous (oe): 1.27 ? (gnomAD)

Ensembl transcript ID

ENST00000509061.5

Genbank transcript ID

NM_001267039 (by similarity)

UniProt / AlphaMissense peptide

LARP7_HUMAN | AlphaMissense: transcript, gene

Variant type

Insertion

Gene region

CDS

DNA changes

c.208_209insAT
g.9280_9281insAT

AA changes

S72Yfs*10

Frameshift

Yes

Length of protein

NMD

Pathogenic variant (ClinVar)

Microcephalic primordial dwarfism, Alazami type

pathogenic

Variant DBs

	Not in dbSNP
	Allele 'AT' was not found in gnomAD

Protein conservation

Species	Match	AA	Alignment
Human		72	I	E	K	S	R	D	G	Y	V	D	I	S	L	L	V	S	F	N	K	M	K	K	L	T
mutated	no alignment	n/a
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	582	CHAIN		lost
28	122	DOMAIN	HTH La-type RNA-binding	lost
71	75	HELIX		lost
78	81	HELIX		lost
87	93	HELIX		lost
106	110	STRAND		lost
122	125	HELIX		lost
125	203	DOMAIN	RRM	lost
127	130	STRAND		lost
137	146	HELIX		lost
151	155	STRAND		lost
160	162	STRAND		lost
167	175	STRAND		lost
176	183	HELIX		lost
184	187	TURN		lost
188	368	REGION		lost
237	237	CROSSLNK	Glycyl lysine isopeptide (Lys-Gly)	lost
239	254	COMPBIAS	Polar residues	lost
257	257	MOD_RES	Phosphothreonine	lost
258	258	MOD_RES	Phosphoserine	lost
261	261	MOD_RES	Phosphoserine	lost
268	353	COMPBIAS	Basic and acidic residues	lost
273	273	MOD_RES	Phosphoserine	lost
298	298	MOD_RES	Phosphoserine	lost
299	299	MOD_RES	Phosphoserine	lost
300	300	MOD_RES	Phosphoserine	lost
337	337	MOD_RES	Phosphoserine	lost
338	338	MOD_RES	Phosphothreonine	lost
351	351	MOD_RES	Phosphoserine	lost
410	410	CROSSLNK	Glycyl lysine isopeptide (Lys-Gly)	lost
410	429	COMPBIAS	Polar residues	lost
410	442	REGION		lost
450	563	DOMAIN	xRRM	lost
456	463	STRAND		lost
468	476	HELIX		lost
481	485	STRAND		lost
491	499	STRAND		lost
500	508	HELIX		lost
510	515	HELIX		lost
519	523	STRAND		lost
526	544	HELIX		lost
551	555	STRAND		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	9.286	1
(flanking)	8.653	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

7

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

4

Strand

1

Original gDNA sequence snippet

TTCATTTTCTTTAGATGTTGATATATCACTACTTGTGTCT

Altered gDNA sequence snippet

TTCATTTTCTTTAGATGTTGATATATATCACTACTTGTGTCT

Original cDNA sequence snippet

ATCTAGAGATGGATATGTTGATATATCACTACTTGTGTCT

Altered cDNA sequence snippet

ATCTAGAGATGGATATGTTGATATATATCACTACTTGTGTCT

Wildtype AA sequence

METESGNQEK VMEEESTEKK KEVEKKKRSR VKQVLADIAK QVDFWFGDAN LHKDRFLREQ
IEKSRDGYVD ISLLVSFNKM KKLTTDGKLI ARALRSSAVV ELDLEGTRIR RKKPLGERPK
DEDERTVYVE LLPKNVNHSW IERVFGKCGN VVYISIPHYK STGDPKGFAF VEFETKEQAA
KAIEFLNNPP EEAPRKPGIF PKTVKNKPIP ALRVVEEKKK KKKKKGRMKK EDNIQAKEEN
MDTSNTSISK MKRSRPTSEG SDIESTEPQK QCSKKKKKRD RVEASSLPEV RTGKRKRSSS
EDAESLAPRS KVKKIIQKDI IKEASEASKE NRDIEISTEE EKDTGDLKDS SLLKTKRKHK
KKHKERHKMG EEVIPLRVLS KSEWMDLKKE YLALQKASMA SLKKTISQIK SESEMETDSG
VPQNTGMKNE KTANREECRT QEKVNATGPQ FVSGVIVKII STEPLPGRKQ VRDTLAAISE
VLYVDLLEGD TECHARFKTP EDAQAVINAY TEINKKHCWK LEILSGDHEQ RYWQKILVDR
QAKLNQPREK KRGTEKLITK AEKIRLAKTQ QASKHIRFSE YD*

Mutated AA sequence

METESGNQEK VMEEESTEKK KEVEKKKRSR VKQVLADIAK QVDFWFGDAN LHKDRFLREQ
IEKSRDGYVD IYHYLCLLTK *

Position of stopcodon in wt / mu CDS

1749 / 243

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

583 / 81

Position of stopcodon in wt / mu cDNA

2073 / 567

Position of start ATG in wt / mu cDNA

325 / 325

Last intron/exon boundary

1992

Theoretical NMD boundary in CDS

1617

Length of CDS

1749

Coding sequence (CDS) position

208 / 209

cDNA position

532 / 533

gDNA position

9280 / 9281

Chromosomal position

112646356 / 112646357

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

MutationT@ster 2025

Variant:

4:112646356G>GAT_5_ENST00000511529

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Frameshift
Known disease mutation: ClinVar ID 374899 (pathogenic)
NMD

Model: complex_aae
Tree vote: 10|0 (del | benign) ?
Automatic classification due to ClinVar

Analysed issue

Analysis result

Variant

Chr4:112646356_112646357insAT (GRCh38)

Gene symbol

Gene constraints

LOEUF: 1.09, LOF (oe): 0.82, misssense (oe): 1.11, synonymous (oe): 1.26 ? (gnomAD)

Ensembl transcript ID

ENST00000511529.2

Genbank transcript ID

NM_001370976 (by similarity), NM_001370977 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Insertion

Gene region

CDS

DNA changes

c.208_209insAT
g.9280_9281insAT

AA changes

S72Yfs*10

Frameshift

Yes

Length of protein

NMD

Pathogenic variant (ClinVar)

Microcephalic primordial dwarfism, Alazami type

pathogenic

Variant DBs

	Not in dbSNP
	Allele 'AT' was not found in gnomAD

Protein conservation

Species	Match	AA	Alignment
Human		72	I	E	K	S	R	D	G	Y	V	D	I	S	L	L	V	S	F	N	K	M	K	K	L	T
mutated	no alignment	n/a
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)	9.286	1
(flanking)	8.653	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

7

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

4

Strand

1

Original gDNA sequence snippet

TTCATTTTCTTTAGATGTTGATATATCACTACTTGTGTCT

Altered gDNA sequence snippet

TTCATTTTCTTTAGATGTTGATATATATCACTACTTGTGTCT

Original cDNA sequence snippet

ATCTAGAGATGGATATGTTGATATATCACTACTTGTGTCT

Altered cDNA sequence snippet

ATCTAGAGATGGATATGTTGATATATATCACTACTTGTGTCT

Wildtype AA sequence

METESGNQEK VMEEESTEKK KEVEKKKRSR VKQVLADIAK QVDFWFGDAN LHKDRFLREQ
IEKSRDGYVD ISLLVSFNKM KKLTTDGKLI ARALRSSAVV ELDLEGTRIR RKKPLGERPK
DEDERTVYVE LLPKNVNHSW IERVFGKCGN VVYISIPHYK STGDPKGFAF VEFETKEQAA
KAIEFLNNPP EEAPRKPGIF PKTVKNKPIP ALRVVEKKKK KKKKGRMKKE DNIQAKEENM
DTSNTSISKM KRSRPTSEGS DIESTEPQKQ CSKKKKKRDR VEASSLPEVR TGKRKRSSSE
DAESLAPRSK VKKIIQKDII KEASEASKEN RAPCLNGELF YLFQDIEIST EEEKDTGDLK
DSSLLKTKRK HKKKHKERHK MGEEVIPLRV LSKSEWMDLK KEYLALQKAS MASLKKTISQ
IKSESEMETD SGVPQNTGMK NEKTANREEC RTQEKVNATG PQFVSGVIVK IISTEPLPGR
KQVRDTLAAI SEVLYVDLLE GDTECHARFK TPEDAQAVIN AYTEINKKHC WKLEILSGDH
EQRYWQKILV DRQAKLNQPR EKKRGTEKLI TKAEKIRLAK TQQASKHIRF SEYD*

Mutated AA sequence

METESGNQEK VMEEESTEKK KEVEKKKRSR VKQVLADIAK QVDFWFGDAN LHKDRFLREQ
IEKSRDGYVD IYHYLCLLTK *

Position of stopcodon in wt / mu CDS

1785 / 243

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

595 / 81

Position of stopcodon in wt / mu cDNA

1874 / 332

Position of start ATG in wt / mu cDNA

90 / 90

Last intron/exon boundary

1793

Theoretical NMD boundary in CDS

1653

Length of CDS

1785

Coding sequence (CDS) position

208 / 209

cDNA position

297 / 298

gDNA position

9280 / 9281

Chromosomal position

112646356 / 112646357

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

MutationT@ster 2025

Variant:

4:112646356G>GAT_6_ENST00000505034

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Frameshift
Known disease mutation: ClinVar ID 374899 (pathogenic)
NMD
Protein features (might be) affected

Model: complex_aae
Tree vote: 10|0 (del | benign) ?
Automatic classification due to ClinVar

Analysed issue

Analysis result

Variant

Chr4:112646356_112646357insAT (GRCh38)

Gene symbol

Gene constraints

LOEUF: 0.97, LOF (oe): 0.57, misssense (oe): 1.10, synonymous (oe): 1.38 ? (gnomAD)

Ensembl transcript ID

ENST00000505034.6

Genbank transcript ID

NM_015454 (by similarity)

UniProt / AlphaMissense peptide

LARP7_HUMAN | AlphaMissense: transcript, gene

Variant type

Insertion

Gene region

CDS

DNA changes

c.208_209insAT
g.9280_9281insAT

AA changes

S72Yfs*10

Frameshift

Yes

Length of protein

NMD

Pathogenic variant (ClinVar)

Microcephalic primordial dwarfism, Alazami type

pathogenic

Variant DBs

	Not in dbSNP
	Allele 'AT' was not found in gnomAD

Protein conservation

Species	Match	AA	Alignment
Human		72	I	E	K	S	R	D	G	Y	V	D	I	S	L	L	V	S	F	N	K	M	K	K	L	T
mutated	no alignment	n/a
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	582	CHAIN		lost
28	122	DOMAIN	HTH La-type RNA-binding	lost
71	75	HELIX		lost
78	81	HELIX		lost
87	93	HELIX		lost
106	110	STRAND		lost
122	125	HELIX		lost
125	203	DOMAIN	RRM	lost
127	130	STRAND		lost
137	146	HELIX		lost
151	155	STRAND		lost
160	162	STRAND		lost
167	175	STRAND		lost
176	183	HELIX		lost
184	187	TURN		lost
188	368	REGION		lost
237	237	CROSSLNK	Glycyl lysine isopeptide (Lys-Gly)	lost
239	254	COMPBIAS	Polar residues	lost
257	257	MOD_RES	Phosphothreonine	lost
258	258	MOD_RES	Phosphoserine	lost
261	261	MOD_RES	Phosphoserine	lost
268	353	COMPBIAS	Basic and acidic residues	lost
273	273	MOD_RES	Phosphoserine	lost
298	298	MOD_RES	Phosphoserine	lost
299	299	MOD_RES	Phosphoserine	lost
300	300	MOD_RES	Phosphoserine	lost
337	337	MOD_RES	Phosphoserine	lost
338	338	MOD_RES	Phosphothreonine	lost
351	351	MOD_RES	Phosphoserine	lost
410	410	CROSSLNK	Glycyl lysine isopeptide (Lys-Gly)	lost
410	429	COMPBIAS	Polar residues	lost
410	442	REGION		lost
450	563	DOMAIN	xRRM	lost
456	463	STRAND		lost
468	476	HELIX		lost
481	485	STRAND		lost
491	499	STRAND		lost
500	508	HELIX		lost
510	515	HELIX		lost
519	523	STRAND		lost
526	544	HELIX		lost
551	555	STRAND		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	9.286	1
(flanking)	8.653	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

7

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

4

Strand

1

Original gDNA sequence snippet

TTCATTTTCTTTAGATGTTGATATATCACTACTTGTGTCT

Altered gDNA sequence snippet

TTCATTTTCTTTAGATGTTGATATATATCACTACTTGTGTCT

Original cDNA sequence snippet

ATCTAGAGATGGATATGTTGATATATCACTACTTGTGTCT

Altered cDNA sequence snippet

ATCTAGAGATGGATATGTTGATATATATCACTACTTGTGTCT

Wildtype AA sequence

METESGNQEK VMEEESTEKK KEVEKKKRSR VKQVLADIAK QVDFWFGDAN LHKDRFLREQ
IEKSRDGYVD ISLLVSFNKM KKLTTDGKLI ARALRSSAVV ELDLEGTRIR RKKPLGERPK
DEDERTVYVE LLPKNVNHSW IERVFGKCGN VVYISIPHYK STGDPKGFAF VEFETKEQAA
KAIEFLNNPP EEAPRKPGIF PKTVKNKPIP ALRVVEEKKK KKKKKGRMKK EDNIQAKEEN
MDTSNTSISK MKRSRPTSEG SDIESTEPQK QCSKKKKKRD RVEASSLPEV RTGKRKRSSS
EDAESLAPRS KVKKIIQKDI IKEASEASKE NRDIEISTEE EKDTGDLKDS SLLKTKRKHK
KKHKERHKMG EEVIPLRVLS KSEWMDLKKE YLALQKASMA SLKKTISQIK SESEMETDSG
VPQNTGMKNE KTANREECRT QEKVNATGPQ FVSGVIVKII STEPLPGRKQ VRDTLAAISE
VLYVDLLEGD TECHARFKTP EDAQAVINAY TEINKKHCWK LEILSGDHEQ RYWQKILVDR
QAKLNQPREK KRGTEKLITK AEKIRLAKTQ QASKHIRFSE YD*

Mutated AA sequence

METESGNQEK VMEEESTEKK KEVEKKKRSR VKQVLADIAK QVDFWFGDAN LHKDRFLREQ
IEKSRDGYVD IYHYLCLLTK *

Position of stopcodon in wt / mu CDS

1749 / 243

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

583 / 81

Position of stopcodon in wt / mu cDNA

1899 / 393

Position of start ATG in wt / mu cDNA

151 / 151

Last intron/exon boundary

1818

Theoretical NMD boundary in CDS

1617

Length of CDS

1749

Coding sequence (CDS) position

208 / 209

cDNA position

358 / 359

gDNA position

9280 / 9281

Chromosomal position

112646356 / 112646357

Speed

0.04 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

MutationT@ster 2025

Variant:

4:112646356G>GAT_8_ENST00000694896

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Frameshift
Known disease mutation: ClinVar ID 374899 (pathogenic)
NMD

Model: complex_aae
Tree vote: 10|0 (del | benign) ?
Automatic classification due to ClinVar

Analysed issue

Analysis result

Variant

Chr4:112646356_112646357insAT (GRCh38)

Gene symbol

Gene constraints

no data

Ensembl transcript ID

ENST00000694896.1

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Insertion

Gene region

CDS

DNA changes

c.208_209insAT
g.9280_9281insAT

AA changes

S72Yfs*10

Frameshift

Yes

Length of protein

NMD

Pathogenic variant (ClinVar)

Microcephalic primordial dwarfism, Alazami type

pathogenic

Variant DBs

	Not in dbSNP
	Allele 'AT' was not found in gnomAD

Protein conservation

Species	Match	AA	Alignment
Human		72	I	E	K	S	R	D	G	Y	V	D	I	S	L	L	V	S	F	N	K	M	K	K	L	T
mutated	no alignment	n/a
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)	9.286	1
(flanking)	8.653	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

7

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

4

Strand

1

Original gDNA sequence snippet

TTCATTTTCTTTAGATGTTGATATATCACTACTTGTGTCT

Altered gDNA sequence snippet

TTCATTTTCTTTAGATGTTGATATATATCACTACTTGTGTCT

Original cDNA sequence snippet

ATCTAGAGATGGATATGTTGATATATCACTACTTGTGTCT

Altered cDNA sequence snippet

ATCTAGAGATGGATATGTTGATATATATCACTACTTGTGTCT

Wildtype AA sequence

METESGNQEK VMEEESTEKK KEVEKKKRSR VKQVLADIAK QVDFWFGDAN LHKDRFLREQ
IEKSRDGYVD ISLLVSFNKM KKLTTDGKLI ARALRSSAVV ELDLEGTRIR RKKPLGERPK
DEDERTVYVE LLPKNVNHSW IERVFGKCGN VVYISIPHYK STGDPKGFAF VEFETKEQAA
KAIEFLNNPP EEAPRKPGIF PKTVKNKPIP ALRVVEEKKK KKKKKGRMKK EDNIQAKEEN
MDTSNTSISK MKRSRPTSEG SDIESTEPQK QCSKKKKKRD RVEASSLPEV RTGKRKRSSS
EDAESLAPRS KVKKIIQKDI IKEASEASKE NRAPCLNGEL FYLFQDIEIS TEEEKDTGDL
KDSSLLKTKR KHKKKHKERH KMGEEVIPLR VLSKSEWMDL KKEYLALQKA SMASLKKTIS
QIKSESEMET DSGVPQNTGM KNEKTNREEC RTQEKVNATG PQFVSGVIVK IISTEPLPGR
KQVRDTLAAI SEVLYVDLLE GDTECHARFK TPEDAQAVIN AYTEINKKHC WKLEILSGDH
EQRYWQKILV DRQAKLNQPR EKKRGTEKLI TKAEKIRLAK TQQASKHIRF SEYD*

Mutated AA sequence

METESGNQEK VMEEESTEKK KEVEKKKRSR VKQVLADIAK QVDFWFGDAN LHKDRFLREQ
IEKSRDGYVD IYHYLCLLTK *

Position of stopcodon in wt / mu CDS

1785 / 243

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

595 / 81

Position of stopcodon in wt / mu cDNA

2936 / 1394

Position of start ATG in wt / mu cDNA

1152 / 1152

Last intron/exon boundary

2855

Theoretical NMD boundary in CDS

1653

Length of CDS

1785

Coding sequence (CDS) position

208 / 209

cDNA position

1359 / 1360

gDNA position

9280 / 9281

Chromosomal position

112646356 / 112646357

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

MutationT@ster 2025

Variant:

4:112646356G>GAT_9_ENST00000694898

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Frameshift
Known disease mutation: ClinVar ID 374899 (pathogenic)
NMD

Model: complex_aae
Tree vote: 10|0 (del | benign) ?
Automatic classification due to ClinVar

Analysed issue

Analysis result

Variant

Chr4:112646356_112646357insAT (GRCh38)

Gene symbol

Gene constraints

no data

Ensembl transcript ID

ENST00000694898.1

Genbank transcript ID

NM_001370974 (by similarity), NM_001370975 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Insertion

Gene region

CDS

DNA changes

c.208_209insAT
g.9280_9281insAT

AA changes

S72Yfs*10

Frameshift

Yes

Length of protein

NMD

Pathogenic variant (ClinVar)

Microcephalic primordial dwarfism, Alazami type

pathogenic

Variant DBs

	Not in dbSNP
	Allele 'AT' was not found in gnomAD

Protein conservation

Species	Match	AA	Alignment
Human		72	I	E	K	S	R	D	G	Y	V	D	I	S	L	L	V	S	F	N	K	M	K	K	L	T
mutated	no alignment	n/a
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)	9.286	1
(flanking)	8.653	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

7

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

4

Strand

1

Original gDNA sequence snippet

TTCATTTTCTTTAGATGTTGATATATCACTACTTGTGTCT

Altered gDNA sequence snippet

TTCATTTTCTTTAGATGTTGATATATATCACTACTTGTGTCT

Original cDNA sequence snippet

ATCTAGAGATGGATATGTTGATATATCACTACTTGTGTCT

Altered cDNA sequence snippet

ATCTAGAGATGGATATGTTGATATATATCACTACTTGTGTCT

Wildtype AA sequence

METESGNQEK VMEEESTEKK KEVEKKKRSR VKQVLADIAK QVDFWFGDAN LHKDRFLREQ
IEKSRDGYVD ISLLVSFNKM KKLTTDGKLI ARALRSSAVV ELDLEGTRIR RKKPLGERPK
DEDERTVYVE LLPKNVNHSW IERVFGKCGN VVYISIPHYK STGDPKGFAF VEFETKEQAA
KAIEFLNNPP EEAPRKPGIF PKTVKNKPIP ALRVVEEKKK KKKKKGRMKK EDNIQAKEEN
MDTSNTSISK MKRSRPTSEG SDIESTEPQK QCSKKKKKRD RVEASSLPEV RTGKRKRSSS
EDAESLAPRS KVKKIIQKDI IKEASEASKE NRAPCLNGEL FYLFQDIEIS TEEEKDTGDL
KDSSLLKTKR KHKKKHKERH KMGEEVIPLR VLSKSEWMDL KKEYLALQKA SMASLKKTIS
QIKSESEMET DSGVPQNTGM KNEKTANREE CRTQEKVNAT GPQFVSGVIV KIISTEPLPG
RKQVRDTLAA ISEVLYVDLL EGDTECHARF KTPEDAQAVI NAYTEINKKH CWKLEILSGD
HEQRYWQKIL VDRQAKLNQP REKKRGTEKL ITKAEKIRLA KTQQASKHIR FSEYD*

Mutated AA sequence

METESGNQEK VMEEESTEKK KEVEKKKRSR VKQVLADIAK QVDFWFGDAN LHKDRFLREQ
IEKSRDGYVD IYHYLCLLTK *

Position of stopcodon in wt / mu CDS

1788 / 243

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

596 / 81

Position of stopcodon in wt / mu cDNA

2939 / 1394

Position of start ATG in wt / mu cDNA

1152 / 1152

Last intron/exon boundary

2858

Theoretical NMD boundary in CDS

1656

Length of CDS

1788

Coding sequence (CDS) position

208 / 209

cDNA position

1359 / 1360

gDNA position

9280 / 9281

Chromosomal position

112646356 / 112646357

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

MutationT@ster 2025

Variant:

4:112646356G>GAT_3_ENST00000344442

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Frameshift
Known disease mutation: ClinVar ID 374899 (pathogenic)
NMD
Protein features (might be) affected

Model: complex_aae
Tree vote: 10|0 (del | benign) ?
Automatic classification due to ClinVar

Analysed issue

Analysis result

Variant

Chr4:112646356_112646357insAT (GRCh38)

Gene symbol

Gene constraints

LOEUF: 1.13, LOF (oe): 0.85, misssense (oe): 1.12, synonymous (oe): 1.27 ? (gnomAD)

Ensembl transcript ID

ENST00000344442.10

Genbank transcript ID

NM_016648 (exact from MANE)

UniProt / AlphaMissense peptide

LARP7_HUMAN | AlphaMissense: transcript, gene

Variant type

Insertion

Gene region

CDS

DNA changes

c.208_209insAT
g.9280_9281insAT

AA changes

S72Yfs*10

Frameshift

Yes

Length of protein

NMD

Pathogenic variant (ClinVar)

Microcephalic primordial dwarfism, Alazami type

pathogenic

Variant DBs

	Not in dbSNP
	Allele 'AT' was not found in gnomAD

Protein conservation

Species	Match	AA	Alignment
Human		72	I	E	K	S	R	D	G	Y	V	D	I	S	L	L	V	S	F	N	K	M	K	K	L	T	T	D	G	K	L	I	A	R	A	L	R	S	S	A	V	V	E	L	D	L	E	G	T	R	I	R	R	K	K	P	L	G	E	R	P	K	D	E	D	E	R	T	V	Y	V	E	L	L	P	K	N	V	N	H	S	W	I	E	R	V	F	G	K	C	G	N	V	V	Y	I	S	I	P	H	Y	K	S	T	G	D	P	K	G	F	A	F	V	E	F	E	T	K	E	Q	A	A	K	A	I	E	F	L	N	N	P	P	E	E	A	P	R
mutated	no alignment	n/a
Ptroglodytes	all identical	79	I	E	K	S	R	D	G	Y	V	D	I	S	L	L	V	S	F	N	K	M	K	K	L	T	T	D	G	K	L	I	A	R	A	L	R	S	S	A	V	V	E	L	D	L	E	G	T	R	I	R	R	K	K	P	L	G	E	R	P	K	D	E	D	E	R	T	V	Y	V	E	L	L	P	K	N	V	N	H	S	W	I	E	R	V	F	G	K	C	G	N	V	V	Y	I	S	I	P	H	Y	K	S	T	G	D	P	K	G	F	A	F	V	E	F	E	T	K	E	Q	A	A
Mmulatta	all identical	72	I	E	K	S	R	D	G	Y	V	D	I	S	L	L	V	S	F	N	K	M	K	K	L	T	T	D	G	K	L	I	A	R	A	L	R	S	S	A	V	V	E	L	D	L	E	G	T	R	I	R	R	K	K	P	L	G	E	R	P	K	D	E	D	E	R	T	V	Y	V	E	L	L	P	K	N	V	N	H	S	W	I	E	R	V	F	G	K	C	G	N	V	V	Y	I	S	I	P	H	Y	K	S	T	G	D	P	K	G	F	A	F	V	E	F	E	T	K	E	Q	A	A
Fcatus	all conserved	72	I	E	K	S	R	D	G	Y	V	D	I	S	L	L	V	S	F	N	K	M	K	K	L	T	T	D	G	K	L	I	A	R	A	L	K	S	S	S	V	V	E	L	D	L	E	G	T	R	I	R	R	K	K	P	L	G	E	R	P	K	D	E	D	E	R	T	V	Y	V	E	L	L	P	K	N	V	N	H	S	W	I	E	R	V	F	G	K	C	G	N	V	V	Y	I	S	I	P	H	Y	K	S	T	G	D	P	K	G	F	A	F	V	E	F	E	T	K	E	Q	A	A
Mmusculus	partly conserved	66	I	E	K	S	R	D	G	Y	V	D	I	S	L	L	V	S	F	N	K	M	K	K	L	T	T	D	G	K	L	I	A	R	A	L	K	S	S	S	V	V	E	L	D	L	E	G	T	R	I	R	R	K	K	P	L	G	E	R	P	K	D	E	E	E	R	T	V	Y	V	E	L	L	P	K	N	V	T	H	S	W	I	E	R	V	F	G	K	C	G	N	V	V	Y	I	S	I	P	H	Y	K	S	T	G	D	P	K	G	F	A	F	V	E	F	E	T	K	E	Q	A	A
Ggallus	partly conserved	126	I	E	K	S	R	D	G	Y	V	D	I	S	L	L	V	S	F	N	K	M	K	K	L	T	T	D	G	K	L	I	A	R	A	V	K	S	S	S	V	V	E	L	D	L	E	G	T	R	I	R	R	R	R	P	L	G	E	R	P	K	D	V	D	S	R	T	V	Y	V	E	L	L	P	K	N	V	N	H	S	W	I	E	R	V	F	G	K	C	G	N	V	V	Y	V	S	I	P	R	Y	K	S	T	G	D	P	K	G	F	A	F	V	E	F	E	T	K	E	Q	A	E
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	partly conserved	97				-	-	D	P	Y	V	P	L	E	I	F	L	T	F	N	K	I	K	T	L	T	Q	D	V	Q	Q	I	A	K	A	L	S	N	S	Q	L	L	E	L	D	E	T	E	L	K	V	K	R	R	T	K	L	P	D	Q	-	R	D	V	N	D	K	T	L	Y	V	E	A	L	P	A	N	A	T	H	D	W	L	K	E	V	F	S	R	Y	G	P	V	A	Y	V	S	L	P	H	Y	P	G	T	K	K	I	K	E	F	A	F	I	E	F	E	K	S	G	S	L	E	K	A	V
Celegans	no homologue
Xtropicalis	partly conserved	74	I	E	K	T	R	D	G	Y	I	D	I	S	L	L	A	S	F	N	K	M	K	K	I	T	T	D	S	K	L	I	A	R	A	V	K	N	S	S	V	V	E	I	N	L	S	G	T	K	I	R	R	R	F	P	L	G	E	K	P	Q	D	V	D	S	R	T	V	Y	V	E	L	L	P	K	N	V	T	H	S	W	I	E	R	V	F	G	K	Y	G	M	V	V	Y	V	S	I	P	R	Y	K	S	T	G	D	P	K	G	F	A	F	I	E	F	E	T	Q	E	Q	A	A

Protein features

Start (aa)	End (aa)	Feature	Details
1	582	CHAIN		lost
28	122	DOMAIN	HTH La-type RNA-binding	lost
71	75	HELIX		lost
78	81	HELIX		lost
87	93	HELIX		lost
106	110	STRAND		lost
122	125	HELIX		lost
125	203	DOMAIN	RRM	lost
127	130	STRAND		lost
137	146	HELIX		lost
151	155	STRAND		lost
160	162	STRAND		lost
167	175	STRAND		lost
176	183	HELIX		lost
184	187	TURN		lost
188	368	REGION		lost
237	237	CROSSLNK	Glycyl lysine isopeptide (Lys-Gly)	lost
239	254	COMPBIAS	Polar residues	lost
257	257	MOD_RES	Phosphothreonine	lost
258	258	MOD_RES	Phosphoserine	lost
261	261	MOD_RES	Phosphoserine	lost
268	353	COMPBIAS	Basic and acidic residues	lost
273	273	MOD_RES	Phosphoserine	lost
298	298	MOD_RES	Phosphoserine	lost
299	299	MOD_RES	Phosphoserine	lost
300	300	MOD_RES	Phosphoserine	lost
337	337	MOD_RES	Phosphoserine	lost
338	338	MOD_RES	Phosphothreonine	lost
351	351	MOD_RES	Phosphoserine	lost
410	410	CROSSLNK	Glycyl lysine isopeptide (Lys-Gly)	lost
410	429	COMPBIAS	Polar residues	lost
410	442	REGION		lost
450	563	DOMAIN	xRRM	lost
456	463	STRAND		lost
468	476	HELIX		lost
481	485	STRAND		lost
491	499	STRAND		lost
500	508	HELIX		lost
510	515	HELIX		lost
519	523	STRAND		lost
526	544	HELIX		lost
551	555	STRAND		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	9.286	1
(flanking)	8.653	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

7

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

4

Strand

1

Original gDNA sequence snippet

TTCATTTTCTTTAGATGTTGATATATCACTACTTGTGTCT

Altered gDNA sequence snippet

TTCATTTTCTTTAGATGTTGATATATATCACTACTTGTGTCT

Original cDNA sequence snippet

ATCTAGAGATGGATATGTTGATATATCACTACTTGTGTCT

Altered cDNA sequence snippet

ATCTAGAGATGGATATGTTGATATATATCACTACTTGTGTCT

Wildtype AA sequence

METESGNQEK VMEEESTEKK KEVEKKKRSR VKQVLADIAK QVDFWFGDAN LHKDRFLREQ
IEKSRDGYVD ISLLVSFNKM KKLTTDGKLI ARALRSSAVV ELDLEGTRIR RKKPLGERPK
DEDERTVYVE LLPKNVNHSW IERVFGKCGN VVYISIPHYK STGDPKGFAF VEFETKEQAA
KAIEFLNNPP EEAPRKPGIF PKTVKNKPIP ALRVVEEKKK KKKKKGRMKK EDNIQAKEEN
MDTSNTSISK MKRSRPTSEG SDIESTEPQK QCSKKKKKRD RVEASSLPEV RTGKRKRSSS
EDAESLAPRS KVKKIIQKDI IKEASEASKE NRDIEISTEE EKDTGDLKDS SLLKTKRKHK
KKHKERHKMG EEVIPLRVLS KSEWMDLKKE YLALQKASMA SLKKTISQIK SESEMETDSG
VPQNTGMKNE KTANREECRT QEKVNATGPQ FVSGVIVKII STEPLPGRKQ VRDTLAAISE
VLYVDLLEGD TECHARFKTP EDAQAVINAY TEINKKHCWK LEILSGDHEQ RYWQKILVDR
QAKLNQPREK KRGTEKLITK AEKIRLAKTQ QASKHIRFSE YD*

Mutated AA sequence

METESGNQEK VMEEESTEKK KEVEKKKRSR VKQVLADIAK QVDFWFGDAN LHKDRFLREQ
IEKSRDGYVD IYHYLCLLTK *

Position of stopcodon in wt / mu CDS

1749 / 243

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

583 / 81

Position of stopcodon in wt / mu cDNA

1848 / 342

Position of start ATG in wt / mu cDNA

100 / 100

Last intron/exon boundary

1767

Theoretical NMD boundary in CDS

1617

Length of CDS

1749

Coding sequence (CDS) position

208 / 209

cDNA position

307 / 308

gDNA position

9280 / 9281

Chromosomal position

112646356 / 112646357

Speed

0.07 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

MutationT@ster 2025

Variant:

4:112646356G>GAT_10_ENST00000694899

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Frameshift
Known disease mutation: ClinVar ID 374899 (pathogenic)
NMD

Model: complex_aae
Tree vote: 10|0 (del | benign) ?
Automatic classification due to ClinVar

Analysed issue

Analysis result

Variant

Chr4:112646356_112646357insAT (GRCh38)

Gene symbol

Gene constraints

no data

Ensembl transcript ID

ENST00000694899.1

Genbank transcript ID

NM_001370980 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Insertion

Gene region

CDS

DNA changes

c.208_209insAT
g.9280_9281insAT

AA changes

S72Yfs*10

Frameshift

Yes

Length of protein

NMD

Pathogenic variant (ClinVar)

Microcephalic primordial dwarfism, Alazami type

pathogenic

Variant DBs

	Not in dbSNP
	Allele 'AT' was not found in gnomAD

Protein conservation

Species	Match	AA	Alignment
Human		72	I	E	K	S	R	D	G	Y	V	D	I	S	L	L	V	S	F	N	K	M	K	K	L	T
mutated	no alignment	n/a
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)	9.286	1
(flanking)	8.653	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

7

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

4

Strand

1

Original gDNA sequence snippet

TTCATTTTCTTTAGATGTTGATATATCACTACTTGTGTCT

Altered gDNA sequence snippet

TTCATTTTCTTTAGATGTTGATATATATCACTACTTGTGTCT

Original cDNA sequence snippet

ATCTAGAGATGGATATGTTGATATATCACTACTTGTGTCT

Altered cDNA sequence snippet

ATCTAGAGATGGATATGTTGATATATATCACTACTTGTGTCT

Wildtype AA sequence

METESGNQEK VMEEESTEKK KEVEKKKRSR VKQVLADIAK QVDFWFGDAN LHKDRFLREQ
IEKSRDGYVD ISLLVSFNKM KKLTTDGKLI ARALRSSAVV ELDLEGTRIR RKKPLGERPK
DEDERTVYVE LLPKNVNHSW IERVFGKCGN VVYISIPHYK STGDPKGFAF VEFETKEQAA
KAIEFLNNPP EEAPRKPGIF PKTVKNKPIP ALRVVEKKKK KKKKGRMKKE DNIQAKEENM
DTSNTSISKM KRSRPTSEGS DIESTEPQKQ CSKKKKKRDR VEASSLPEVR TGKRKRSSSE
DAESLAPRSK VKKIIQKDII KEASEASKEN RDIEISTEEE KDTGDLKDSS LLKTKRKHKK
KHKERHKMGE EVIPLRVLSK SEWMDLKKEY LALQKASMAS LKKTISQIKS ESEMETDSGV
PQNTGMKNEK TANREECRTQ EKVNATGPQF VSGVIVKIIS TEPLPGRKQV RDTLAAISEV
LYVDLLEGDT ECHARFKTPE DAQAVINAYT EINKKHCWKL EILSGDHEQR YWQKILVDRQ
AKLNQPREKK RGTEKLITKA EKIRLAKTQQ ASKHIRFSEY D*

Mutated AA sequence

METESGNQEK VMEEESTEKK KEVEKKKRSR VKQVLADIAK QVDFWFGDAN LHKDRFLREQ
IEKSRDGYVD IYHYLCLLTK *

Position of stopcodon in wt / mu CDS

1746 / 243

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

582 / 81

Position of stopcodon in wt / mu cDNA

2897 / 1394

Position of start ATG in wt / mu cDNA

1152 / 1152

Last intron/exon boundary

2816

Theoretical NMD boundary in CDS

1614

Length of CDS

1746

Coding sequence (CDS) position

208 / 209

cDNA position

1359 / 1360

gDNA position

9280 / 9281

Chromosomal position

112646356 / 112646357

Speed

0.04 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

MutationT@ster 2025

Variant:

4:112646356G>GAT_11_ENST00000694900

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Frameshift
Known disease mutation: ClinVar ID 374899 (pathogenic)
NMD

Model: complex_aae
Tree vote: 10|0 (del | benign) ?
Automatic classification due to ClinVar

Analysed issue

Analysis result

Variant

Chr4:112646356_112646357insAT (GRCh38)

Gene symbol

Gene constraints

no data

Ensembl transcript ID

ENST00000694900.1

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Insertion

Gene region

CDS

DNA changes

c.208_209insAT
g.9280_9281insAT

AA changes

S72Yfs*10

Frameshift

Yes

Length of protein

NMD

Pathogenic variant (ClinVar)

Microcephalic primordial dwarfism, Alazami type

pathogenic

Variant DBs

	Not in dbSNP
	Allele 'AT' was not found in gnomAD

Protein conservation

Species	Match	AA	Alignment
Human		72	I	E	K	S	R	D	G	Y	V	D	I	S	L	L	V	S	F	N	K	M	K	K	L	T
mutated	no alignment	n/a
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)	9.286	1
(flanking)	8.653	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

7

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

4

Strand

1

Original gDNA sequence snippet

TTCATTTTCTTTAGATGTTGATATATCACTACTTGTGTCT

Altered gDNA sequence snippet

TTCATTTTCTTTAGATGTTGATATATATCACTACTTGTGTCT

Original cDNA sequence snippet

ATCTAGAGATGGATATGTTGATATATCACTACTTGTGTCT

Altered cDNA sequence snippet

ATCTAGAGATGGATATGTTGATATATATCACTACTTGTGTCT

Wildtype AA sequence

METESGNQEK VMEEESTEKK KEVEKKKRSR VKQVLADIAK QVDFWFGDAN LHKDRFLREQ
IEKSRDGYVD ISLLVSFNKM KKLTTDGKLI ARALRSSAVV ELDLEGTRIR RKKPLGERPK
DEDERTVYVE LLPKNVNHSW IERVFGKCGN VVYISIPHYK STGDPKGFAF VEFETKEQAA
KAIEFLNNPP EEAPRKPGIF PKTVKNKPIP ALRVVEEKKK KKKKKGRMKK EDNIQAKEEN
MDTSNTSISK MKRSRPTSEG SDIESTEPQK QCSKKKKKRD RVEASSLPEV RTGKRKRSSS
EDAESLAPRS KVKKIIQKDI IKEASEASKE NREISTEEEK DTGDLKDSSL LKTKRKHKKK
HKERHKMGEE VIPLRVLSKS EWMDLKKEYL ALQKASMASL KKTISQIKSE SEMETDSGVP
QNTGMKNEKT ANREECRTQE KVNATGPQFV SGVIVKIIST EPLPGRKQVR DTLAAISEVL
YVDLLEGDTE CHARFKTPED AQAVINAYTE INKKHCWKLE ILSGDHEQRY WQKILVDRQA
KLNQPREKKR GTEKLITKAE KIRLAKTQQA SKHIRFSEYD *

Mutated AA sequence

METESGNQEK VMEEESTEKK KEVEKKKRSR VKQVLADIAK QVDFWFGDAN LHKDRFLREQ
IEKSRDGYVD IYHYLCLLTK *

Position of stopcodon in wt / mu CDS

1743 / 243

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

581 / 81

Position of stopcodon in wt / mu cDNA

2894 / 1394

Position of start ATG in wt / mu cDNA

1152 / 1152

Last intron/exon boundary

2813

Theoretical NMD boundary in CDS

1611

Length of CDS

1743

Coding sequence (CDS) position

208 / 209

cDNA position

1359 / 1360

gDNA position

9280 / 9281

Chromosomal position

112646356 / 112646357

Speed

0.04 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

MutationT@ster 2025

Variant:

4:112646356G>GAT_13_ENST00000694895

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Frameshift
Known disease mutation: ClinVar ID 374899 (pathogenic)
NMD

Model: complex_aae
Tree vote: 10|0 (del | benign) ?
Automatic classification due to ClinVar

Analysed issue

Analysis result

Variant

Chr4:112646356_112646357insAT (GRCh38)

Gene symbol

Gene constraints

no data

Ensembl transcript ID

ENST00000694895.1

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Insertion

Gene region

CDS

DNA changes

c.208_209insAT
g.9280_9281insAT

AA changes

S72Yfs*10

Frameshift

Yes

Length of protein

NMD

Pathogenic variant (ClinVar)

Microcephalic primordial dwarfism, Alazami type

pathogenic

Variant DBs

	Not in dbSNP
	Allele 'AT' was not found in gnomAD

Protein conservation

Species	Match	AA	Alignment
Human		72	I	E	K	S	R	D	G	Y	V	D	I	S	L	L	V	S	F	N	K	M	K	K	L	T
mutated	no alignment	n/a
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)	9.286	1
(flanking)	8.653	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

7

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

4

Strand

1

Original gDNA sequence snippet

TTCATTTTCTTTAGATGTTGATATATCACTACTTGTGTCT

Altered gDNA sequence snippet

TTCATTTTCTTTAGATGTTGATATATATCACTACTTGTGTCT

Original cDNA sequence snippet

ATCTAGAGATGGATATGTTGATATATCACTACTTGTGTCT

Altered cDNA sequence snippet

ATCTAGAGATGGATATGTTGATATATATCACTACTTGTGTCT

Wildtype AA sequence

METESGNQEK VMEEESTEKK KEVEKKKRSR VKQVLADIAK QVDFWFGDAN LHKDRFLREQ
IEKSRDGYVD ISLLVSFNKM KKLTTDGKLI ARALRSSAVV ELDLEGTRIR RKKPLGERPK
DEDERTVYVE LLPKNVNHSW IERVFGKCGN VVYISIPHYK STGDPKGFAF VEFETKEQAA
KAIEFLNNPP EEAPRKPGIF PKTVKNKPIP ALRVVEEKKK KKKKKGRMKK EDNIQAKEEN
MDTSNTSISK MKRSRPTSEG SDIESTEPQK QCSKKKKKRD RVEASSLPEV RTGKRKRSSS
EDAESLAPRS KVKKIIQKDI IKEASEASKE NRDIEISTEE EKDTGDLKDS SLLKTKRKHK
KKHKERHKMG EEVIPLRVLS KSEWMDLKKE YLALQKASMA SLKKTISQIK SESEMETDSG
VPQNTGMKNE KTNREECRTQ EKVNATGPQF VSGVIVKIIS TEPLPGRKQV RDTLAAISEV
LYVDLLEGDT ECHARFKTPE DAQAVINAYT EINKKHCWKL EILSGDHEQR YWQKILVDRQ
AKLNQPREKK RGTEKLITKA EKIRLAKTQQ ASKHIRFSEY D*

Mutated AA sequence

METESGNQEK VMEEESTEKK KEVEKKKRSR VKQVLADIAK QVDFWFGDAN LHKDRFLREQ
IEKSRDGYVD IYHYLCLLTK *

Position of stopcodon in wt / mu CDS

1746 / 243

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

582 / 81

Position of stopcodon in wt / mu cDNA

1830 / 327

Position of start ATG in wt / mu cDNA

85 / 85

Last intron/exon boundary

1749

Theoretical NMD boundary in CDS

1614

Length of CDS

1746

Coding sequence (CDS) position

208 / 209

cDNA position

292 / 293

gDNA position

9280 / 9281

Chromosomal position

112646356 / 112646357

Speed

0.04 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

MutationT@ster 2025

Variant:

4:112646356G>GAT_12_ENST00000651579

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Frameshift
Known disease mutation: ClinVar ID 374899 (pathogenic)
NMD
Protein features (might be) affected

Model: complex_aae
Tree vote: 10|0 (del | benign) ?
Automatic classification due to ClinVar

Analysed issue

Analysis result

Variant

Chr4:112646356_112646357insAT (GRCh38)

Gene symbol

Gene constraints

LOEUF: 1.13, LOF (oe): 0.85, misssense (oe): 1.12, synonymous (oe): 1.27 ? (gnomAD)

Ensembl transcript ID

ENST00000651579.1

Genbank transcript ID

NM_001370978 (by similarity)

UniProt / AlphaMissense peptide

LARP7_HUMAN | AlphaMissense: transcript, gene

Variant type

Insertion

Gene region

CDS

DNA changes

c.208_209insAT
g.9280_9281insAT

AA changes

S72Yfs*10

Frameshift

Yes

Length of protein

NMD

Pathogenic variant (ClinVar)

Microcephalic primordial dwarfism, Alazami type

pathogenic

Variant DBs

	Not in dbSNP
	Allele 'AT' was not found in gnomAD

Protein conservation

Species	Match	AA	Alignment
Human		72	I	E	K	S	R	D	G	Y	V	D	I	S	L	L	V	S	F	N	K	M	K	K	L	T
mutated	no alignment	n/a
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	582	CHAIN		lost
28	122	DOMAIN	HTH La-type RNA-binding	lost
71	75	HELIX		lost
78	81	HELIX		lost
87	93	HELIX		lost
106	110	STRAND		lost
122	125	HELIX		lost
125	203	DOMAIN	RRM	lost
127	130	STRAND		lost
137	146	HELIX		lost
151	155	STRAND		lost
160	162	STRAND		lost
167	175	STRAND		lost
176	183	HELIX		lost
184	187	TURN		lost
188	368	REGION		lost
237	237	CROSSLNK	Glycyl lysine isopeptide (Lys-Gly)	lost
239	254	COMPBIAS	Polar residues	lost
257	257	MOD_RES	Phosphothreonine	lost
258	258	MOD_RES	Phosphoserine	lost
261	261	MOD_RES	Phosphoserine	lost
268	353	COMPBIAS	Basic and acidic residues	lost
273	273	MOD_RES	Phosphoserine	lost
298	298	MOD_RES	Phosphoserine	lost
299	299	MOD_RES	Phosphoserine	lost
300	300	MOD_RES	Phosphoserine	lost
337	337	MOD_RES	Phosphoserine	lost
338	338	MOD_RES	Phosphothreonine	lost
351	351	MOD_RES	Phosphoserine	lost
410	410	CROSSLNK	Glycyl lysine isopeptide (Lys-Gly)	lost
410	429	COMPBIAS	Polar residues	lost
410	442	REGION		lost
450	563	DOMAIN	xRRM	lost
456	463	STRAND		lost
468	476	HELIX		lost
481	485	STRAND		lost
491	499	STRAND		lost
500	508	HELIX		lost
510	515	HELIX		lost
519	523	STRAND		lost
526	544	HELIX		lost
551	555	STRAND		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	9.286	1
(flanking)	8.653	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

7

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

4

Strand

1

Original gDNA sequence snippet

TTCATTTTCTTTAGATGTTGATATATCACTACTTGTGTCT

Altered gDNA sequence snippet

TTCATTTTCTTTAGATGTTGATATATATCACTACTTGTGTCT

Original cDNA sequence snippet

ATCTAGAGATGGATATGTTGATATATCACTACTTGTGTCT

Altered cDNA sequence snippet

ATCTAGAGATGGATATGTTGATATATATCACTACTTGTGTCT

Wildtype AA sequence

METESGNQEK VMEEESTEKK KEVEKKKRSR VKQVLADIAK QVDFWFGDAN LHKDRFLREQ
IEKSRDGYVD ISLLVSFNKM KKLTTDGKLI ARALRSSAVV ELDLEGTRIR RKKPLGERPK
DEDERTVYVE LLPKNVNHSW IERVFGKCGN VVYISIPHYK STGDPKGFAF VEFETKEQAA
KAIEFLNNPP EEAPRKPGIF PKTVKNKPIP ALRVVEEKKK KKKKKGRMKK EDNIQAKEEN
MDTSNTSISK MKRSRPTSEG SDIESTEPQK QCSKKKKKRD RVEASSLPEV RTGKRKRSSS
EDAESLAPRS KVKKIIQKDI IKEASEASKE NRDIEISTEE EKDTGDLKDS SLLKTKRKHK
KKHKERHKMG EEVIPLRVLS KSEWMDLKKE YLALQKASMA SLKKTISQIK SESEMETDSG
VPQNTGMKNE KTANREECRT QEKVNATGPQ FVSGVIVKII STEPLPGRKQ VRDTLAAISE
VLYVDLLEGD TECHARFKTP EDAQAVINAY TEINKKHCWK LEILSGDHEQ RYWQKILVDR
QAKLNQPREK KRGTEKLITK AEKIRLAKTQ QASKHIRFSE YD*

Mutated AA sequence

METESGNQEK VMEEESTEKK KEVEKKKRSR VKQVLADIAK QVDFWFGDAN LHKDRFLREQ
IEKSRDGYVD IYHYLCLLTK *

Position of stopcodon in wt / mu CDS

1749 / 243

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

583 / 81

Position of stopcodon in wt / mu cDNA

1841 / 335

Position of start ATG in wt / mu cDNA

93 / 93

Last intron/exon boundary

1760

Theoretical NMD boundary in CDS

1617

Length of CDS

1749

Coding sequence (CDS) position

208 / 209

cDNA position

300 / 301

gDNA position

9280 / 9281

Chromosomal position

112646356 / 112646357

Speed

0.04 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

MutationT@ster 2025

Variant:

4:112646356G>GAT_14_ENST00000694894

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Frameshift
Known disease mutation: ClinVar ID 374899 (pathogenic)
NMD
Protein features (might be) affected

Model: complex_aae
Tree vote: 10|0 (del | benign) ?
Automatic classification due to ClinVar

Analysed issue

Analysis result

Variant

Chr4:112646356_112646357insAT (GRCh38)

Gene symbol

Gene constraints

no data

Ensembl transcript ID

ENST00000694894.1

Genbank transcript ID

UniProt / AlphaMissense peptide

LARP7_HUMAN | AlphaMissense: transcript, gene

Variant type

Insertion

Gene region

CDS

DNA changes

c.208_209insAT
g.9280_9281insAT

AA changes

S72Yfs*10

Frameshift

Yes

Length of protein

NMD

Pathogenic variant (ClinVar)

Microcephalic primordial dwarfism, Alazami type

pathogenic

Variant DBs

	Not in dbSNP
	Allele 'AT' was not found in gnomAD

Protein conservation

Species	Match	AA	Alignment
Human		72	I	E	K	S	R	D	G	Y	V	D	I	S	L	L	V	S	F	N	K	M	K	K	L	T
mutated	no alignment	n/a
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	582	CHAIN		lost
28	122	DOMAIN	HTH La-type RNA-binding	lost
71	75	HELIX		lost
78	81	HELIX		lost
87	93	HELIX		lost
106	110	STRAND		lost
122	125	HELIX		lost
125	203	DOMAIN	RRM	lost
127	130	STRAND		lost
137	146	HELIX		lost
151	155	STRAND		lost
160	162	STRAND		lost
167	175	STRAND		lost
176	183	HELIX		lost
184	187	TURN		lost
188	368	REGION		lost
237	237	CROSSLNK	Glycyl lysine isopeptide (Lys-Gly)	lost
239	254	COMPBIAS	Polar residues	lost
257	257	MOD_RES	Phosphothreonine	lost
258	258	MOD_RES	Phosphoserine	lost
261	261	MOD_RES	Phosphoserine	lost
268	353	COMPBIAS	Basic and acidic residues	lost
273	273	MOD_RES	Phosphoserine	lost
298	298	MOD_RES	Phosphoserine	lost
299	299	MOD_RES	Phosphoserine	lost
300	300	MOD_RES	Phosphoserine	lost
337	337	MOD_RES	Phosphoserine	lost
338	338	MOD_RES	Phosphothreonine	lost
351	351	MOD_RES	Phosphoserine	lost
410	410	CROSSLNK	Glycyl lysine isopeptide (Lys-Gly)	lost
410	429	COMPBIAS	Polar residues	lost
410	442	REGION		lost
450	563	DOMAIN	xRRM	lost
456	463	STRAND		lost
468	476	HELIX		lost
481	485	STRAND		lost
491	499	STRAND		lost
500	508	HELIX		lost
510	515	HELIX		lost
519	523	STRAND		lost
526	544	HELIX		lost
551	555	STRAND		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	9.286	1
(flanking)	8.653	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

7

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

4

Strand

1

Original gDNA sequence snippet

TTCATTTTCTTTAGATGTTGATATATCACTACTTGTGTCT

Altered gDNA sequence snippet

TTCATTTTCTTTAGATGTTGATATATATCACTACTTGTGTCT

Original cDNA sequence snippet

ATCTAGAGATGGATATGTTGATATATCACTACTTGTGTCT

Altered cDNA sequence snippet

ATCTAGAGATGGATATGTTGATATATATCACTACTTGTGTCT

Wildtype AA sequence

METESGNQEK VMEEESTEKK KEVEKKKRSR VKQVLADIAK QVDFWFGDAN LHKDRFLREQ
IEKSRDGYVD ISLLVSFNKM KKLTTDGKLI ARALRSSAVV ELDLEGTRIR RKKPLGERPK
DEDERTVYVE LLPKNVNHSW IERVFGKCGN VVYISIPHYK STGDPKGFAF VEFETKEQAA
KAIEFLNNPP EEAPRKPGIF PKTVKNKPIP ALRVVEEKKK KKKKKGRMKK EDNIQAKEEN
MDTSNTSISK MKRSRPTSEG SDIESTEPQK QCSKKKKKRD RVEASSLPEV RTGKRKRSSS
EDAESLAPRS KVKKIIQKDI IKEASEASKE NRDIEISTEE EKDTGDLKDS SLLKTKRKHK
KKHKERHKMG EEVIPLRVLS KSEWMDLKKE YLALQKASMA SLKKTISQIK SESEMETDSG
VPQNTGMKNE KTANREECRT QEKVNATGPQ FVSGVIVKII STEPLPGRKQ VRDTLAAISE
VLYVDLLEGD TECHARFKTP EDAQAVINAY TEINKKHCWK LEILSGDHEQ RYWQKILVDR
QAKLNQPREK KRGTEKLITK AEKIRLAKTQ QASKHIRFSE YD*

Mutated AA sequence

METESGNQEK VMEEESTEKK KEVEKKKRSR VKQVLADIAK QVDFWFGDAN LHKDRFLREQ
IEKSRDGYVD IYHYLCLLTK *

Position of stopcodon in wt / mu CDS

1749 / 243

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

583 / 81

Position of stopcodon in wt / mu cDNA

2907 / 1401

Position of start ATG in wt / mu cDNA

1159 / 1159

Last intron/exon boundary

2826

Theoretical NMD boundary in CDS

1617

Length of CDS

1749

Coding sequence (CDS) position

208 / 209

cDNA position

1366 / 1367

gDNA position

9280 / 9281

Chromosomal position

112646356 / 112646357

Speed

0.04 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

MutationT@ster 2025

Variant:

4:112646356G>GAT_4_ENST00000692416

Prediction:

DeleteriousPermalink

Summary:

Known disease mutation: ClinVar ID 374899 (pathogenic)

Model: 5utr
Tree vote: 100|0 (del | benign) ?
Automatic classification due to ClinVar

Analysed issue

Analysis result

Variant

Chr4:112646356_112646357insAT (GRCh38)

Gene symbol

Gene constraints

LOEUF: 1.26, LOF (oe): 0.94, misssense (oe): 1.16, synonymous (oe): 1.27 ? (gnomAD)

Ensembl transcript ID

ENST00000692416.1

Genbank transcript ID

NM_001370982 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Insertion

Gene region

5'UTR

DNA changes

cDNA.187_188insAT
g.9280_9281insAT

AA changes

N/A

Frameshift

No

Length of protein

N/A

Pathogenic variant (ClinVar)

Microcephalic primordial dwarfism, Alazami type

pathogenic

Variant DBs

	Not in dbSNP
	Allele 'AT' was not found in gnomAD

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	9.286	1
(flanking)	8.653	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

7

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

4

Strand

1

Original gDNA sequence snippet

TTCATTTTCTTTAGATGTTGATATATCACTACTTGTGTCT

Altered gDNA sequence snippet

TTCATTTTCTTTAGATGTTGATATATATCACTACTTGTGTCT

Original cDNA sequence snippet

GAAATCAGGAAAAGATGTTGATATATCACTACTTGTGTCT

Altered cDNA sequence snippet

GAAATCAGGAAAAGATGTTGATATATATCACTACTTGTGTCT

Wildtype AA sequence

MKKLTTDGKL IARALRSSAV VELDLEGTRI RRKKPLGERP KDEDERTVYV ELLPKNVNHS
WIERVFGKCG NVVYISIPHY KSTGDPKGFA FVEFETKEQA AKAIEFLNNP PEEAPRKPGI
FPKTVKNKPI PALRVVEEKK KKKKKKGRMK KEDNIQAKEE NMDTSNTSIS KMKRSRPTSE
GSDIESTEPQ KQCSKKKKKR DRVEASSLPE VRTGKRKRSS SEDAESLAPR SKVKKIIQKD
IIKEASEASK ENRDIEISTE EEKDTGDLKD SSLLKTKRKH KKKHKERHKM GEEVIPLRVL
SKSEWMDLKK EYLALQKASM ASLKKTISQI KSESEMETDS GVPQNTGMKN EKTANREECR
TQEKVNATGP QFVSGVIVKI ISTEPLPGRK QVRDTLAAIS EVLYVDLLEG DTECHARFKT
PEDAQAVINA YTEINKKHCW KLEILSGDHE QRYWQKILVD RQAKLNQPRE KKRGTEKLIT
KAEKIRLAKT QQASKHIRFS EYD*

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

217 / 217

Last intron/exon boundary

1647

Theoretical NMD boundary in CDS

1380

Length of CDS

1512

Coding sequence (CDS) position

N/A

cDNA position

187 / 188

gDNA position

9280 / 9281

Chromosomal position

112646356 / 112646357

Speed

0.01 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

MutationT@ster 2025

Variant:

4:112646356G>GAT_7_ENST00000693375

Prediction:

DeleteriousPermalink

Summary:

Known disease mutation: ClinVar ID 374899 (pathogenic)

Model: 5utr
Tree vote: 100|0 (del | benign) ?
Automatic classification due to ClinVar

Analysed issue

Analysis result

Variant

Chr4:112646356_112646357insAT (GRCh38)

Gene symbol

Gene constraints

LOEUF: 1.26, LOF (oe): 0.94, misssense (oe): 1.16, synonymous (oe): 1.27 ? (gnomAD)

Ensembl transcript ID

ENST00000693375.1

Genbank transcript ID

NM_001370981 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Insertion

Gene region

5'UTR

DNA changes

cDNA.88_89insAT
g.9280_9281insAT

AA changes

N/A

Frameshift

No

Length of protein

N/A

Pathogenic variant (ClinVar)

Microcephalic primordial dwarfism, Alazami type

pathogenic

Variant DBs

	Not in dbSNP
	Allele 'AT' was not found in gnomAD

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	9.286	1
(flanking)	8.653	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

7

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

4

Strand

1

Original gDNA sequence snippet

TTCATTTTCTTTAGATGTTGATATATCACTACTTGTGTCT

Altered gDNA sequence snippet

TTCATTTTCTTTAGATGTTGATATATATCACTACTTGTGTCT

Original cDNA sequence snippet

AGAAGATAGCGAACATGTTGATATATCACTACTTGTGTCT

Altered cDNA sequence snippet

AGAAGATAGCGAACATGTTGATATATATCACTACTTGTGTCT

Wildtype AA sequence

MKKLTTDGKL IARALRSSAV VELDLEGTRI RRKKPLGERP KDEDERTVYV ELLPKNVNHS
WIERVFGKCG NVVYISIPHY KSTGDPKGFA FVEFETKEQA AKAIEFLNNP PEEAPRKPGI
FPKTVKNKPI PALRVVEEKK KKKKKKGRMK KEDNIQAKEE NMDTSNTSIS KMKRSRPTSE
GSDIESTEPQ KQCSKKKKKR DRVEASSLPE VRTGKRKRSS SEDAESLAPR SKVKKIIQKD
IIKEASEASK ENRDIEISTE EEKDTGDLKD SSLLKTKRKH KKKHKERHKM GEEVIPLRVL
SKSEWMDLKK EYLALQKASM ASLKKTISQI KSESEMETDS GVPQNTGMKN EKTANREECR
TQEKVNATGP QFVSGVIVKI ISTEPLPGRK QVRDTLAAIS EVLYVDLLEG DTECHARFKT
PEDAQAVINA YTEINKKHCW KLEILSGDHE QRYWQKILVD RQAKLNQPRE KKRGTEKLIT
KAEKIRLAKT QQASKHIRFS EYD*

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

118 / 118

Last intron/exon boundary

1548

Theoretical NMD boundary in CDS

1380

Length of CDS

1512

Coding sequence (CDS) position

N/A

cDNA position

88 / 89

gDNA position

9280 / 9281

Chromosomal position

112646356 / 112646357

Speed

0.01 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