MutationT @ ster 2025

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Known disease mutation: ClinVar ID 208639 (pathogenic)
NMD

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

Analysed issue

Analysis result

Variant

Chr15:89293963A>T (GRCh38)

Gene symbol

Gene constraints

no data

Ensembl transcript ID

ENST00000696718.1

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.1885A>T
g.50019A>T

AA changes

K629* Score: 6.0?

Frameshift

No

Length of protein

NMD

Pathogenic variant (ClinVar)

Fanconi anemia complementation group I
Fanconi anemia

pathogenic

Variant DBs

dbSNP ID	rs375656231
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	0	63	63

Protein conservation

Species	Match	AA	Alignment
Human		629	A	N	K	T	S	D	S	L	L	S	M	K	F	V	S	S	L	L	T	A	L	F	R	D
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)	6.055	1
	4.55	1
(flanking)	4.724	1

?

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

15

Strand

1

Original gDNA sequence snippet

GTGATAGTCTTTTGTCCATGAAATTTGTGTCCAGTCTTCTC

Altered gDNA sequence snippet

GTGATAGTCTTTTGTCCATGTAATTTGTGTCCAGTCTTCTC

Original cDNA sequence snippet

GTGATAGTCTTTTGTCCATGAAATTTGTGTCCAGTCTTCTC

Altered cDNA sequence snippet

GTGATAGTCTTTTGTCCATGTAATTTGTGTCCAGTCTTCTC

Wildtype AA sequence

MFKDVPLTAE EVEFVVEKAL SMFSKMNLQE IPPLVYQLLV LSSKGSRKSV LEGIIAFFSA
LDKQHNEEQS GDELLDVVTV PSGELRHVEG TIILHIVFAI KLDYELGREL VKHLKVGQQG
DSNNNLSPFS IALLLSVTRI QRFQDQVLDL LKTSVVKSFK DLQLLQGSKF LQNLVPHRSY
VSTMILEVVK NSVHSWDHVT QGLVELGFIL MDSYGPKKVL DGKTIETSPS LSRMPNQHAC
KLGANILLET FKIHEMIRQE ILEQVLNRVV TRASSPISHF LDLLSNIVMY APLVLQSCSS
KVTEAFDYLS FLPLQTVQRL LKAVQPLLKV SMSMRDCLIL VLRKAMFANQ LDARKSAVAG
FLLLLKNFKV LGSLSSSQCS QSLSVSQVHV DVHSHYNSVA NETFCLEIMD SLRRCLSQQA
DVRLMLYEGF YDVLRRNSQL ANSVMQTLLS QLKQFYEPKP DLLPPLKLEA CILTQGDKIS
LQEPLDYLLC CIQHCLAWYK NTVIPLQQGE EEEEEEEAFY EDLDDILESI TNRMIKSELE
DFELDKSADF SQSTSIGIKN NICAFLVMGV CEVLIEYNFS ISSFSKNRFE DILSLFMCYK
KLSDILNEKA GKAKTKMANK TSDSLLSMKF VSSLLTALFR DSIQSHQESL SVLRSSNEFM
RYAVNVALQK VQQLKETGHV SGPDGQNPEK IFQNLCDITR VLLWRYTSIP TSVEESGKKE
KGKSISLLCL EGLQKIFSAV QQFYQPKIQQ FLRALDVTDK EGEEREDADV SVTQRTAFQI
RQFQRSLLNL LSSQEEDFNS KEALLLVTVL TSLSKLLEPS SPQFVQMLSW TSKICKENSR
EDALFCKSLM NLLFSLHVSY KSPVILLRDL SQDIHGHLGD IDQDVEVEKT NHFAIVNLRT
AAPTVCLLVL SQAEKVLEEV DWLITKLKGQ VSQETLSEEA SSQATLPNQP VEKAIIMQLG
TLLTFFHELV QTALPSGSCV DTLLKDLCKM YTTLTALVRY YLQVCQSSGG IPKNMEKLVK
LSGSHLTPLC YSFISYVQNK SKSLNYTGEK KEKPAAVATA MARVLRETKP IPNLIFAIEQ
YEKFLIHLSK KSKVNLMQHM KLSTSRDFKI KGNILDMVLR EDGEDENEEG TASEHGGQNK
EPAKKKRKK*

Mutated AA sequence

MFKDVPLTAE EVEFVVEKAL SMFSKMNLQE IPPLVYQLLV LSSKGSRKSV LEGIIAFFSA
LDKQHNEEQS GDELLDVVTV PSGELRHVEG TIILHIVFAI KLDYELGREL VKHLKVGQQG
DSNNNLSPFS IALLLSVTRI QRFQDQVLDL LKTSVVKSFK DLQLLQGSKF LQNLVPHRSY
VSTMILEVVK NSVHSWDHVT QGLVELGFIL MDSYGPKKVL DGKTIETSPS LSRMPNQHAC
KLGANILLET FKIHEMIRQE ILEQVLNRVV TRASSPISHF LDLLSNIVMY APLVLQSCSS
KVTEAFDYLS FLPLQTVQRL LKAVQPLLKV SMSMRDCLIL VLRKAMFANQ LDARKSAVAG
FLLLLKNFKV LGSLSSSQCS QSLSVSQVHV DVHSHYNSVA NETFCLEIMD SLRRCLSQQA
DVRLMLYEGF YDVLRRNSQL ANSVMQTLLS QLKQFYEPKP DLLPPLKLEA CILTQGDKIS
LQEPLDYLLC CIQHCLAWYK NTVIPLQQGE EEEEEEEAFY EDLDDILESI TNRMIKSELE
DFELDKSADF SQSTSIGIKN NICAFLVMGV CEVLIEYNFS ISSFSKNRFE DILSLFMCYK
KLSDILNEKA GKAKTKMANK TSDSLLSM*

Position of stopcodon in wt / mu CDS

3450 / 1887

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

1150 / 629

Position of stopcodon in wt / mu cDNA

3947 / 2384

Position of start ATG in wt / mu cDNA

498 / 498

Last intron/exon boundary

3884

Theoretical NMD boundary in CDS

3336

Length of CDS

3450

Coding sequence (CDS) position

1885

cDNA position

2382

gDNA position

50019

Chromosomal position

89293963

Speed

0.12 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:

15:89293963A>T_4_ENST00000696717

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Known disease mutation: ClinVar ID 208639 (pathogenic)
NMD

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

Analysed issue

Analysis result

Variant

Chr15:89293963A>T (GRCh38)

Gene symbol

Gene constraints

no data

Ensembl transcript ID

ENST00000696717.1

Genbank transcript ID

NM_001376910 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.2143A>T
g.50019A>T

AA changes

K715* Score: 6.0?

Frameshift

No

Length of protein

NMD

Pathogenic variant (ClinVar)

Fanconi anemia complementation group I
Fanconi anemia

pathogenic

Variant DBs

dbSNP ID	rs375656231
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	0	63	63

Protein conservation

Species	Match	AA	Alignment
Human		715	A	N	K	T	S	D	S	L	L	S	M	K	F	V	S	S	L	L	T	A	L	F	R	D
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)	6.055	1
	4.55	1
(flanking)	4.724	1

?

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

15

Strand

1

Original gDNA sequence snippet

GTGATAGTCTTTTGTCCATGAAATTTGTGTCCAGTCTTCTC

Altered gDNA sequence snippet

GTGATAGTCTTTTGTCCATGTAATTTGTGTCCAGTCTTCTC

Original cDNA sequence snippet

GTGATAGTCTTTTGTCCATGAAATTTGTGTCCAGTCTTCTC

Altered cDNA sequence snippet

GTGATAGTCTTTTGTCCATGTAATTTGTGTCCAGTCTTCTC

Wildtype AA sequence

MLEAHHFPGP LLVELANEFI SAVREGSLVN GKSLELLPII LTALATKKEN LAYGKGVLSG
EECKKQLINT LCSGRWDQQY VIQLTSMFKD VPLTAEEVEF VVEKALSMFS KMNLQEIPPL
VYQLLVLSSK GSRKSVLEGI IAFFSALDKQ HNEEQSGDEL LDVVTVPSGE LRHVEGTIIL
HIVFAIKLDY ELGRELVKHL KVGQQGDSNN NLSPFSIALL LSVTRIQRFQ DQVLDLLKTS
VVKSFKDLQL LQGSKFLQNL VPHRSYVSTM ILEVVKNSVH SWDHVTQGLV ELGFILMDSY
GPKKVLDGKT IETSPSLSRM PNQHACKLGA NILLETFKIH EMIRQEILEQ VLNRVVTRAS
SPISHFLDLL SNIVMYAPLV LQSCSSKVTE AFDYLSFLPL QTVQRLLKAV QPLLKVSMSM
RDCLILVLRK AMFANQLDAR KSAVAGFLLL LKNFKVLGSL SSSQCSQSLS VSQVHVDVHS
HYNSVANETF CLEIMDSLRR CLSQQADVRL MLYEGFYDVL RRNSQLANSV MQTLLSQLKQ
FYEPKPDLLP PLKLEACILT QGDKISLQEP LDYLLCCIQH CLAWYKNTVI PLQQGEEEEE
EEEAFYEDLD DILESITNRM IKSELEDFEL DKSADFSQST SIGIKNNICA FLVMGVCEVL
IEYNFSISSF SKNRFEDILS LFMCYKKLSD ILNEKAGKAK TKMANKTSDS LLSMKFVSSL
LTALFRDSIQ SHQESLSVLR SSNEFMRYAV NVALQKVQQL KETGHVSGPD GQNPEKIFQN
LCDITRVLLW RYTSIPTSVE ESGKKEKGKS ISLLCLEGLQ KIFSAVQQFY QPKIQQFLRA
LDVTDKEGEE REDADVSVTQ RTAFQIRQFQ RSLLNLLSSQ EEDFNSKEAL LLVTVLTSLS
KLLEPSSPQF VQMLSWTSKI CKENSREDAL FCKSLMNLLF SLHVSYKSPV ILLRDLSQDI
HGHLGDIDQD VEVEKTNHFA IVNLRTAAPT VCLLVLSQAE KVLEEVDWLI TKLKGQVSQE
TLSEEASSQA TLPNQPVEKA IIMQLGTLLT FFHELVQTAL PSGSCVDTLL KDLCKMYTTL
TALVRYYLQV CQSSGGIPKN MEKLVKLSGS HLTPLCYSFI SYVQNKSKSL NYTGEKKEKP
AAVATAMARV LRETKPIPNL IFAIEQYEKF LIHLSKKSKV NLMQHMKLST SRDFKIKGNI
LDMVLREDGE DENEEGTASE HGGQNKEPAK KKRKK*

Mutated AA sequence

MLEAHHFPGP LLVELANEFI SAVREGSLVN GKSLELLPII LTALATKKEN LAYGKGVLSG
EECKKQLINT LCSGRWDQQY VIQLTSMFKD VPLTAEEVEF VVEKALSMFS KMNLQEIPPL
VYQLLVLSSK GSRKSVLEGI IAFFSALDKQ HNEEQSGDEL LDVVTVPSGE LRHVEGTIIL
HIVFAIKLDY ELGRELVKHL KVGQQGDSNN NLSPFSIALL LSVTRIQRFQ DQVLDLLKTS
VVKSFKDLQL LQGSKFLQNL VPHRSYVSTM ILEVVKNSVH SWDHVTQGLV ELGFILMDSY
GPKKVLDGKT IETSPSLSRM PNQHACKLGA NILLETFKIH EMIRQEILEQ VLNRVVTRAS
SPISHFLDLL SNIVMYAPLV LQSCSSKVTE AFDYLSFLPL QTVQRLLKAV QPLLKVSMSM
RDCLILVLRK AMFANQLDAR KSAVAGFLLL LKNFKVLGSL SSSQCSQSLS VSQVHVDVHS
HYNSVANETF CLEIMDSLRR CLSQQADVRL MLYEGFYDVL RRNSQLANSV MQTLLSQLKQ
FYEPKPDLLP PLKLEACILT QGDKISLQEP LDYLLCCIQH CLAWYKNTVI PLQQGEEEEE
EEEAFYEDLD DILESITNRM IKSELEDFEL DKSADFSQST SIGIKNNICA FLVMGVCEVL
IEYNFSISSF SKNRFEDILS LFMCYKKLSD ILNEKAGKAK TKMANKTSDS LLSM*

Position of stopcodon in wt / mu CDS

3708 / 2145

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

1236 / 715

Position of stopcodon in wt / mu cDNA

4066 / 2503

Position of start ATG in wt / mu cDNA

359 / 359

Last intron/exon boundary

4003

Theoretical NMD boundary in CDS

3594

Length of CDS

3708

Coding sequence (CDS) position

2143

cDNA position

2501

gDNA position

50019

Chromosomal position

89293963

Speed

0.13 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:

15:89293963A>T_3_ENST00000676003

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Known disease mutation: ClinVar ID 208639 (pathogenic)
NMD

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

Analysed issue

Analysis result

Variant

Chr15:89293963A>T (GRCh38)

Gene symbol

Gene constraints

LOEUF: 0.97, LOF (oe): 0.84, misssense (oe): 1.05, synonymous (oe): 1.06 ? (gnomAD)

Ensembl transcript ID

ENST00000676003.1

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.2422A>T
g.50019A>T

AA changes

K808* Score: 6.0?

Frameshift

No

Length of protein

NMD

Pathogenic variant (ClinVar)

Fanconi anemia complementation group I
Fanconi anemia

pathogenic

Variant DBs

dbSNP ID	rs375656231
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	0	63	63

Protein conservation

Species	Match	AA	Alignment
Human		808	A	N	K	T	S	D	S	L	L	S	M	K	F	V	S	S	L	L	T	A	L	F	R	S
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)	6.055	1
	4.55	1
(flanking)	4.724	1

?

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

15

Strand

1

Original gDNA sequence snippet

GTGATAGTCTTTTGTCCATGAAATTTGTGTCCAGTCTTCTC

Altered gDNA sequence snippet

GTGATAGTCTTTTGTCCATGTAATTTGTGTCCAGTCTTCTC

Original cDNA sequence snippet

GTGATAGTCTTTTGTCCATGAAATTTGTGTCCAGTCTTCTC

Altered cDNA sequence snippet

GTGATAGTCTTTTGTCCATGTAATTTGTGTCCAGTCTTCTC

Wildtype AA sequence

MDQKILSLAA EKTADKLQEF LQTLREGDLT NLLQNQAVKG KVAGALLRAI FKGSPCSEEA
GTLRRRKIYT CCIQLVESGD LQKEIASEII GLLMLEAHHF PGPLLVELAN EFISAVREGS
LVNGKSLELL PIILTALATK KENLAYGKGV LSGEECKKQL INTLCSGRWD QQYVIQLTSM
FKDVPLTAEE VEFVVEKALS MFSKMNLQEI PPLVYQLLVL SSKGSRKSVL EGIIAFFSAL
DKQHNEEQSG DELLDVVTVP SGELRHVEGT IILHIVFAIK LDYELGRELV KHLKVGQQGD
SNNNLSPFSI ALLLSVTRIQ RFQDQVLDLL KTSVVKSFKD LQLLQGSKFL QNLVPHRSYV
STMILEVVKN SVHSWDHVTQ GLVELGFILM DSYGPKKVLD GKTIETSPSL SRMPNQHACK
LGANILLETF KIHEMIRQEI LEQVLNRVVT RASSPISHFL DLLSNIVMYA PLVLQSCSSK
VTEAFDYLSF LPLQTVQRLL KAVQPLLKVS MSMRDCLILV LRKAMFANQL DARKSAVAGF
LLLLKNFKVL GSLSSSQCSQ SLSVSQVHVD VHSHYNSVAN ETFCLEIMDS LRRCLSQQAD
VRLMLYEGFY DVLRRNSQLA NSVMQTLLSQ LKQFYEPKPD LLPPLKLEAC ILTQGDKISL
QEPLDYLLCC IQHCLAWYKN TVIPLQQGEE EEEEEEAFYE DLDDILESIT NRMIKSELED
FELDKSADFS QSTSIGIKNN ICAFLVMGVC EVLIEYNFSI SSFSKNRFED ILSLFMCYKK
LSDILNEKAG KAKTKMANKT SDSLLSMKFV SSLLTALFRS SNEFMRYAVN VALQKVQQLK
ETGHVSGPDG QNPEKIFQNL CDITRVLLWR YTSIPTSVEE SGKKEKGKSI SLLCLEGLQK
IFSAVQQFYQ PKIQQFLRAL DVTDKEGEER EDADVSVTQR TAFQIRQFQR SLLNLLSSQE
EDFNSKEALL LVTVLTSLSK LLEPSSPQFV QMLSWTSKIC KENSREDALF CKSLMNLLFS
LHVSYKSPVI LLRDLSQDIH GHLGDIDQDV EVEKTNHFAI VNLRTAAPTV CLLVLSQAEK
VLEEVDWLIT KLKGQVSQET LSEEASSQAT LPNQPVEKAI IMQLGTLLTF FHELVQTALP
SGSCVDTLLK DLCKMYTTLT ALVRYYLQVC QSSGGIPKNM EKLVKLSGSH LTPLCYSFIS
YVQNKSKSLN YTGEKKEKPA AVATAMARVL RETKPIPNLI FAIEQYEKFL IHLSKKSKVN
LMQHMKLSTS RDFKIKGNIL DMVLREDGED ENEEGTASEH GGQNKEPAKK KRKK*

Mutated AA sequence

MDQKILSLAA EKTADKLQEF LQTLREGDLT NLLQNQAVKG KVAGALLRAI FKGSPCSEEA
GTLRRRKIYT CCIQLVESGD LQKEIASEII GLLMLEAHHF PGPLLVELAN EFISAVREGS
LVNGKSLELL PIILTALATK KENLAYGKGV LSGEECKKQL INTLCSGRWD QQYVIQLTSM
FKDVPLTAEE VEFVVEKALS MFSKMNLQEI PPLVYQLLVL SSKGSRKSVL EGIIAFFSAL
DKQHNEEQSG DELLDVVTVP SGELRHVEGT IILHIVFAIK LDYELGRELV KHLKVGQQGD
SNNNLSPFSI ALLLSVTRIQ RFQDQVLDLL KTSVVKSFKD LQLLQGSKFL QNLVPHRSYV
STMILEVVKN SVHSWDHVTQ GLVELGFILM DSYGPKKVLD GKTIETSPSL SRMPNQHACK
LGANILLETF KIHEMIRQEI LEQVLNRVVT RASSPISHFL DLLSNIVMYA PLVLQSCSSK
VTEAFDYLSF LPLQTVQRLL KAVQPLLKVS MSMRDCLILV LRKAMFANQL DARKSAVAGF
LLLLKNFKVL GSLSSSQCSQ SLSVSQVHVD VHSHYNSVAN ETFCLEIMDS LRRCLSQQAD
VRLMLYEGFY DVLRRNSQLA NSVMQTLLSQ LKQFYEPKPD LLPPLKLEAC ILTQGDKISL
QEPLDYLLCC IQHCLAWYKN TVIPLQQGEE EEEEEEAFYE DLDDILESIT NRMIKSELED
FELDKSADFS QSTSIGIKNN ICAFLVMGVC EVLIEYNFSI SSFSKNRFED ILSLFMCYKK
LSDILNEKAG KAKTKMANKT SDSLLSM*

Position of stopcodon in wt / mu CDS

3945 / 2424

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

1315 / 808

Position of stopcodon in wt / mu cDNA

4128 / 2607

Position of start ATG in wt / mu cDNA

184 / 184

Last intron/exon boundary

4065

Theoretical NMD boundary in CDS

3831

Length of CDS

3945

Coding sequence (CDS) position

2422

cDNA position

2605

gDNA position

50019

Chromosomal position

89293963

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:

15:89293963A>T_1_ENST00000696719

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Known disease mutation: ClinVar ID 208639 (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

Chr15:89293963A>T (GRCh38)

Gene symbol

Gene constraints

no data

Ensembl transcript ID

ENST00000696719.1

Genbank transcript ID

UniProt / AlphaMissense peptide

FANCI_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.2422A>T
g.50019A>T

AA changes

K808* Score: 6.0?

Frameshift

No

Length of protein

NMD

Pathogenic variant (ClinVar)

Fanconi anemia complementation group I
Fanconi anemia

pathogenic

Variant DBs

dbSNP ID	rs375656231
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	0	63	63

Protein conservation

Species	Match	AA	Alignment
Human		808	A	N	K	T	S	D	S	L	L	S	M	K	F	V	S	S	L	L	T	A	L	F	R	D
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	1328	CHAIN		lost
807	818	HELIX		lost
823	833	HELIX		lost
836	856	HELIX		lost
862	865	TURN		lost
867	887	HELIX		lost
897	900	HELIX		lost
904	922	HELIX		lost
924	926	HELIX		lost
927	932	HELIX		lost
951	970	HELIX		lost
952	952	MOD_RES	Phosphothreonine	lost
979	993	HELIX		lost
998	1000	STRAND		lost
1001	1016	HELIX		lost
1022	1037	HELIX		lost
1043	1057	HELIX		lost
1062	1064	STRAND		lost
1077	1083	TURN		lost
1084	1109	HELIX		lost
1121	1121	MOD_RES	Phosphoserine	lost
1128	1148	HELIX		lost
1157	1183	HELIX		lost
1184	1186	TURN		lost
1192	1204	HELIX		lost
1206	1218	HELIX		lost
1237	1245	HELIX		lost
1249	1271	HELIX		lost
1276	1278	TURN		lost
1284	1287	STRAND		lost
1293	1296	HELIX		lost
1300	1328	REGION		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	6.055	1
	4.55	1
(flanking)	4.724	1

?

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

15

Strand

1

Original gDNA sequence snippet

GTGATAGTCTTTTGTCCATGAAATTTGTGTCCAGTCTTCTC

Altered gDNA sequence snippet

GTGATAGTCTTTTGTCCATGTAATTTGTGTCCAGTCTTCTC

Original cDNA sequence snippet

GTGATAGTCTTTTGTCCATGAAATTTGTGTCCAGTCTTCTC

Altered cDNA sequence snippet

GTGATAGTCTTTTGTCCATGTAATTTGTGTCCAGTCTTCTC

Wildtype AA sequence

MDQKILSLAA EKTADKLQEF LQTLREGDLT NLLQNQAVKG KVAGALLRAI FKGSPCSEEA
GTLRRRKIYT CCIQLVESGD LQKEIASEII GLLMLEAHHF PGPLLVELAN EFISAVREGS
LVNGKSLELL PIILTALATK KENLAYGKGV LSGEECKKQL INTLCSGRWD QQYVIQLTSM
FKDVPLTAEE VEFVVEKALS MFSKMNLQEI PPLVYQLLVL SSKGSRKSVL EGIIAFFSAL
DKQHNEEQSG DELLDVVTVP SGELRHVEGT IILHIVFAIK LDYELGRELV KHLKVGQQGD
SNNNLSPFSI ALLLSVTRIQ RFQDQVLDLL KTSVVKSFKD LQLLQGSKFL QNLVPHRSYV
STMILEVVKN SVHSWDHVTQ GLVELGFILM DSYGPKKVLD GKTIETSPSL SRMPNQHACK
LGANILLETF KIHEMIRQEI LEQVLNRVVT RASSPISHFL DLLSNIVMYA PLVLQSCSSK
VTEAFDYLSF LPLQTVQRLL KAVQPLLKVS MSMRDCLILV LRKAMFANQL DARKSAVAGF
LLLLKNFKVL GSLSSSQCSQ SLSVSQVHVD VHSHYNSVAN ETFCLEIMDS LRRCLSQQAD
VRLMLYEGFY DVLRRNSQLA NSVMQTLLSQ LKQFYEPKPD LLPPLKLEAC ILTQGDKISL
QEPLDYLLCC IQHCLAWYKN TVIPLQQGEE EEEEEEAFYE DLDDILESIT NRMIKSELED
FELDKSADFS QSTSIGIKNN ICAFLVMGVC EVLIEYNFSI SSFSKNRFED ILSLFMCYKK
LSDILNEKAG KAKTKMANKT SDSLLSMKFV SSLLTALFRD SIQSHQESLS VLRSSNEFMR
YAVNVALQKV QQLKETGHVS GPDGQNPEKI FQNLCDITRV LLWRYTSIPT SVEESGKKEK
GKSISLLCLE GLQKIFSAVQ QFYQPKIQQF LRALDVTDKE GEEREDADVS VTQRTAFQIR
QFQRSLLNLL SSQEEDFNSK EALLLVTVLT SLSKLLEPSS PQFVQMLSWT SKICKENSRE
DALFCKSLMN LLFSLHVSYK SPVILLRDLS QDIHGHLGDI DQDVEVEKTN HFAIVNLRTA
APTVCLLVLS QAEKVLEEVD WLITKLKGQV SQETLSEEAS SQATLPNQPV EKAIIMQLGT
LLTFFHELVQ TALPSGSCVD TLLKDLCKMY TTLTALVRYY LQVCQSSGGI PKNMEKLVKL
SGSHLTPLCY SFISYVQNKS KSLNYTGEKK EKPAAVATAM ARVLRETKPI PNLIFAIEQY
EKFLIHLSKK SKVNLMQHMK LSTSRDFKIK GNILDMVLRE DGEDENEEGT ASEHGGQNKE
PAKKKRKK*

Mutated AA sequence

MDQKILSLAA EKTADKLQEF LQTLREGDLT NLLQNQAVKG KVAGALLRAI FKGSPCSEEA
GTLRRRKIYT CCIQLVESGD LQKEIASEII GLLMLEAHHF PGPLLVELAN EFISAVREGS
LVNGKSLELL PIILTALATK KENLAYGKGV LSGEECKKQL INTLCSGRWD QQYVIQLTSM
FKDVPLTAEE VEFVVEKALS MFSKMNLQEI PPLVYQLLVL SSKGSRKSVL EGIIAFFSAL
DKQHNEEQSG DELLDVVTVP SGELRHVEGT IILHIVFAIK LDYELGRELV KHLKVGQQGD
SNNNLSPFSI ALLLSVTRIQ RFQDQVLDLL KTSVVKSFKD LQLLQGSKFL QNLVPHRSYV
STMILEVVKN SVHSWDHVTQ GLVELGFILM DSYGPKKVLD GKTIETSPSL SRMPNQHACK
LGANILLETF KIHEMIRQEI LEQVLNRVVT RASSPISHFL DLLSNIVMYA PLVLQSCSSK
VTEAFDYLSF LPLQTVQRLL KAVQPLLKVS MSMRDCLILV LRKAMFANQL DARKSAVAGF
LLLLKNFKVL GSLSSSQCSQ SLSVSQVHVD VHSHYNSVAN ETFCLEIMDS LRRCLSQQAD
VRLMLYEGFY DVLRRNSQLA NSVMQTLLSQ LKQFYEPKPD LLPPLKLEAC ILTQGDKISL
QEPLDYLLCC IQHCLAWYKN TVIPLQQGEE EEEEEEAFYE DLDDILESIT NRMIKSELED
FELDKSADFS QSTSIGIKNN ICAFLVMGVC EVLIEYNFSI SSFSKNRFED ILSLFMCYKK
LSDILNEKAG KAKTKMANKT SDSLLSM*

Position of stopcodon in wt / mu CDS

3987 / 2424

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

1329 / 808

Position of stopcodon in wt / mu cDNA

4163 / 2600

Position of start ATG in wt / mu cDNA

177 / 177

Last intron/exon boundary

4100

Theoretical NMD boundary in CDS

3873

Length of CDS

3987

Coding sequence (CDS) position

2422

cDNA position

2598

gDNA position

50019

Chromosomal position

89293963

Speed

0.14 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:

15:89293963A>T_7_ENST00000674831

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Known disease mutation: ClinVar ID 208639 (pathogenic)
NMD

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

Analysed issue

Analysis result

Variant

Chr15:89293963A>T (GRCh38)

Gene symbol

Gene constraints

LOEUF: 0.96, LOF (oe): 0.83, misssense (oe): 1.05, synonymous (oe): 1.06 ? (gnomAD)

Ensembl transcript ID

ENST00000674831.1

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.2422A>T
g.50019A>T

AA changes

K808* Score: 6.0?

Frameshift

No

Length of protein

NMD

Pathogenic variant (ClinVar)

Fanconi anemia complementation group I
Fanconi anemia

pathogenic

Variant DBs

dbSNP ID	rs375656231
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	0	63	63

Protein conservation

Species	Match	AA	Alignment
Human		808	A	N	K	T	S	D	S	L	L	S	M	K	F	V	S	S	L	L	T	A	L	F	R	D
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)	6.055	1
	4.55	1
(flanking)	4.724	1

?

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

15

Strand

1

Original gDNA sequence snippet

GTGATAGTCTTTTGTCCATGAAATTTGTGTCCAGTCTTCTC

Altered gDNA sequence snippet

GTGATAGTCTTTTGTCCATGTAATTTGTGTCCAGTCTTCTC

Original cDNA sequence snippet

GTGATAGTCTTTTGTCCATGAAATTTGTGTCCAGTCTTCTC

Altered cDNA sequence snippet

GTGATAGTCTTTTGTCCATGTAATTTGTGTCCAGTCTTCTC

Wildtype AA sequence

MDQKILSLAA EKTADKLQEF LQTLREGDLT NLLQNQAVKG KVAGALLRAI FKGSPCSEEA
GTLRRRKIYT CCIQLVESGD LQKEIASEII GLLMLEAHHF PGPLLVELAN EFISAVREGS
LVNGKSLELL PIILTALATK KENLAYGKGV LSGEECKKQL INTLCSGRWD QQYVIQLTSM
FKDVPLTAEE VEFVVEKALS MFSKMNLQEI PPLVYQLLVL SSKGSRKSVL EGIIAFFSAL
DKQHNEEQSG DELLDVVTVP SGELRHVEGT IILHIVFAIK LDYELGRELV KHLKVGQQGD
SNNNLSPFSI ALLLSVTRIQ RFQDQVLDLL KTSVVKSFKD LQLLQGSKFL QNLVPHRSYV
STMILEVVKN SVHSWDHVTQ GLVELGFILM DSYGPKKVLD GKTIETSPSL SRMPNQHACK
LGANILLETF KIHEMIRQEI LEQVLNRVVT RASSPISHFL DLLSNIVMYA PLVLQSCSSK
VTEAFDYLSF LPLQTVQRLL KAVQPLLKVS MSMRDCLILV LRKAMFANQL DARKSAVAGF
LLLLKNFKVL GSLSSSQCSQ SLSVSQVHVD VHSHYNSVAN ETFCLEIMDS LRRCLSQQAD
VRLMLYEGFY DVLRRNSQLA NSVMQTLLSQ LKQFYEPKPD LLPPLKLEAC ILTQGDKISL
QEPLDYLLCC IQHCLAWYKN TVIPLQQGEE EEEEEEAFYE DLDDILESIT NRMIKSELED
FELDKSADFS QSTSIGIKNN ICAFLVMGVC EVLIEYNFSI SSFSKNRFED ILSLFMCYKK
LSDILNEKAG KAKTKMANKT SDSLLSMKFV SSLLTALFRD SIQSHQESLS VLRSSNEFMR
YAVNVALQKV QQLKETGHVS GPDGQNPEKI FQNLCDITRV LLWRYTSIPT SVEESGKKEK
GKSISLLCLE GLQKIFSAVQ QFYQPKIQQF LRALDVTDKE GEEREDADVS VTQRTAFQIR
QFQRSLLNLL SSQEEDFNSK EALLLVTVLT SLSKLLEPSS PQFVQMLSWT SKICKENSRE
DALFCKSLMN LLFSLHVSYK SPVILLRDLS QDIHGHLGDI DQDVEVEKTN HFAIVNLRTA
APTVCLLVLS QAEKVLEEVD WLITKLKGQV SQETLSEEAS SQATLPNQPV EKAIIMQLGT
LLTFFHELVQ TALPSGSCVD TLLKDLCKMY TTLTALVRYY LQVCQSSGGI PKNMEKLVKL
SGSHLTPLCY SFISYVQGQK QITAYQPLWN VCSSLFSRTW HVEQVSCFSH GSSCRASLYF
QNKSKSLNYT GEKKEKPAAV ATAMARVLRE TKPIPNLIFA IEQYEKFLIH LSKKSKVNLM
QHMKLSTSRD FKIKGNILDM VLREDGEDEN EEGTASEHGG QNKEPAKKKR KK*

Mutated AA sequence

MDQKILSLAA EKTADKLQEF LQTLREGDLT NLLQNQAVKG KVAGALLRAI FKGSPCSEEA
GTLRRRKIYT CCIQLVESGD LQKEIASEII GLLMLEAHHF PGPLLVELAN EFISAVREGS
LVNGKSLELL PIILTALATK KENLAYGKGV LSGEECKKQL INTLCSGRWD QQYVIQLTSM
FKDVPLTAEE VEFVVEKALS MFSKMNLQEI PPLVYQLLVL SSKGSRKSVL EGIIAFFSAL
DKQHNEEQSG DELLDVVTVP SGELRHVEGT IILHIVFAIK LDYELGRELV KHLKVGQQGD
SNNNLSPFSI ALLLSVTRIQ RFQDQVLDLL KTSVVKSFKD LQLLQGSKFL QNLVPHRSYV
STMILEVVKN SVHSWDHVTQ GLVELGFILM DSYGPKKVLD GKTIETSPSL SRMPNQHACK
LGANILLETF KIHEMIRQEI LEQVLNRVVT RASSPISHFL DLLSNIVMYA PLVLQSCSSK
VTEAFDYLSF LPLQTVQRLL KAVQPLLKVS MSMRDCLILV LRKAMFANQL DARKSAVAGF
LLLLKNFKVL GSLSSSQCSQ SLSVSQVHVD VHSHYNSVAN ETFCLEIMDS LRRCLSQQAD
VRLMLYEGFY DVLRRNSQLA NSVMQTLLSQ LKQFYEPKPD LLPPLKLEAC ILTQGDKISL
QEPLDYLLCC IQHCLAWYKN TVIPLQQGEE EEEEEEAFYE DLDDILESIT NRMIKSELED
FELDKSADFS QSTSIGIKNN ICAFLVMGVC EVLIEYNFSI SSFSKNRFED ILSLFMCYKK
LSDILNEKAG KAKTKMANKT SDSLLSM*

Position of stopcodon in wt / mu CDS

4119 / 2424

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

1373 / 808

Position of stopcodon in wt / mu cDNA

4227 / 2532

Position of start ATG in wt / mu cDNA

109 / 109

Last intron/exon boundary

4164

Theoretical NMD boundary in CDS

4005

Length of CDS

4119

Coding sequence (CDS) position

2422

cDNA position

2530

gDNA position

50019

Chromosomal position

89293963

Speed

0.13 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:

15:89293963A>T_6_ENST00000300027

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Known disease mutation: ClinVar ID 208639 (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

Chr15:89293963A>T (GRCh38)

Gene symbol

Gene constraints

LOEUF: 0.98, LOF (oe): 0.84, misssense (oe): 1.05, synonymous (oe): 1.05 ? (gnomAD)

Ensembl transcript ID

ENST00000300027.12

Genbank transcript ID

NM_018193 (by similarity)

UniProt / AlphaMissense peptide

FANCI_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.2422A>T
g.50019A>T

AA changes

K808* Score: 6.0?

Frameshift

No

Length of protein

NMD

Pathogenic variant (ClinVar)

Fanconi anemia complementation group I
Fanconi anemia

pathogenic

Variant DBs

dbSNP ID	rs375656231
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	0	63	63

Protein conservation

Species	Match	AA	Alignment
Human		808	A	N	K	T	S	D	S	L	L	S	M	K	F	V	S	S	L	L	T	A	L	F	R	V
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	1328	CHAIN		lost
807	818	HELIX		lost
823	833	HELIX		lost
836	856	HELIX		lost
862	865	TURN		lost
867	887	HELIX		lost
897	900	HELIX		lost
904	922	HELIX		lost
924	926	HELIX		lost
927	932	HELIX		lost
951	970	HELIX		lost
952	952	MOD_RES	Phosphothreonine	lost
979	993	HELIX		lost
998	1000	STRAND		lost
1001	1016	HELIX		lost
1022	1037	HELIX		lost
1043	1057	HELIX		lost
1062	1064	STRAND		lost
1077	1083	TURN		lost
1084	1109	HELIX		lost
1121	1121	MOD_RES	Phosphoserine	lost
1128	1148	HELIX		lost
1157	1183	HELIX		lost
1184	1186	TURN		lost
1192	1204	HELIX		lost
1206	1218	HELIX		lost
1237	1245	HELIX		lost
1249	1271	HELIX		lost
1276	1278	TURN		lost
1284	1287	STRAND		lost
1293	1296	HELIX		lost
1300	1328	REGION		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	6.055	1
	4.55	1
(flanking)	4.724	1

?

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

15

Strand

1

Original gDNA sequence snippet

GTGATAGTCTTTTGTCCATGAAATTTGTGTCCAGTCTTCTC

Altered gDNA sequence snippet

GTGATAGTCTTTTGTCCATGTAATTTGTGTCCAGTCTTCTC

Original cDNA sequence snippet

GTGATAGTCTTTTGTCCATGAAATTTGTGTCCAGTCTTCTC

Altered cDNA sequence snippet

GTGATAGTCTTTTGTCCATGTAATTTGTGTCCAGTCTTCTC

Wildtype AA sequence

MDQKILSLAA EKTADKLQEF LQTLREGDLT NLLQNQAVKG KVAGALLRAI FKGSPCSEEA
GTLRRRKIYT CCIQLVESGD LQKEIASEII GLLMLEAHHF PGPLLVELAN EFISAVREGS
LVNGKSLELL PIILTALATK KENLAYGKGV LSGEECKKQL INTLCSGRWD QQYVIQLTSM
FKDVPLTAEE VEFVVEKALS MFSKMNLQEI PPLVYQLLVL SSKGSRKSVL EGIIAFFSAL
DKQHNEEQSG DELLDVVTVP SGELRHVEGT IILHIVFAIK LDYELGRELV KHLKVGQQGD
SNNNLSPFSI ALLLSVTRIQ RFQDQVLDLL KTSVVKSFKD LQLLQGSKFL QNLVPHRSYV
STMILEVVKN SVHSWDHVTQ GLVELGFILM DSYGPKKVLD GKTIETSPSL SRMPNQHACK
LGANILLETF KIHEMIRQEI LEQVLNRVVT RASSPISHFL DLLSNIVMYA PLVLQSCSSK
VTEAFDYLSF LPLQTVQRLL KAVQPLLKVS MSMRDCLILV LRKAMFANQL DARKSAVAGF
LLLLKNFKVL GSLSSSQCSQ SLSVSQVHVD VHSHYNSVAN ETFCLEIMDS LRRCLSQQAD
VRLMLYEGFY DVLRRNSQLA NSVMQTLLSQ LKQFYEPKPD LLPPLKLEAC ILTQGDKISL
QEPLDYLLCC IQHCLAWYKN TVIPLQQGEE EEEEEEAFYE DLDDILESIT NRMIKSELED
FELDKSADFS QSTSIGIKNN ICAFLVMGVC EVLIEYNFSI SSFSKNRFED ILSLFMCYKK
LSDILNEKAG KAKTKMANKT SDSLLSMKFV SSLLTALFRV LLWRYTSIPT SVEESGKKEK
GKSISLLCLE GLQKIFSAVQ QFYQPKIQQF LRALDVTDKE GEEREDADVS VTQRTAFQIR
QFQRSLLNLL SSQEEDFNSK EALLLVTVLT SLSKLLEPSS PQFVQMLSWT SKICKENSRE
DALFCKSLMN LLFSLHVSYK SPVILLRDLS QDIHGHLGDI DQDVEVEKTN HFAIVNLRTA
APTVCLLVLS QAEKVLEEVD WLITKLKGQV SQETLSEEAS SQATLPNQPV EKAIIMQLGT
LLTFFHELVQ TALPSGSCVD TLLKDLCKMY TTLTALVRYY LQVCQSSGGI PKNMEKLVKL
SGSHLTPLCY SFISYVQNKS KSLNYTGEKK EKPAAVATAM ARVLRETKPI PNLIFAIEQY
EKFLIHLSKK SKVNLMQHMK LSTSRDFKIK GNILDMVLRE DGEDENEEGT ASEHGGQNKE
PAKKKRKK*

Mutated AA sequence

MDQKILSLAA EKTADKLQEF LQTLREGDLT NLLQNQAVKG KVAGALLRAI FKGSPCSEEA
GTLRRRKIYT CCIQLVESGD LQKEIASEII GLLMLEAHHF PGPLLVELAN EFISAVREGS
LVNGKSLELL PIILTALATK KENLAYGKGV LSGEECKKQL INTLCSGRWD QQYVIQLTSM
FKDVPLTAEE VEFVVEKALS MFSKMNLQEI PPLVYQLLVL SSKGSRKSVL EGIIAFFSAL
DKQHNEEQSG DELLDVVTVP SGELRHVEGT IILHIVFAIK LDYELGRELV KHLKVGQQGD
SNNNLSPFSI ALLLSVTRIQ RFQDQVLDLL KTSVVKSFKD LQLLQGSKFL QNLVPHRSYV
STMILEVVKN SVHSWDHVTQ GLVELGFILM DSYGPKKVLD GKTIETSPSL SRMPNQHACK
LGANILLETF KIHEMIRQEI LEQVLNRVVT RASSPISHFL DLLSNIVMYA PLVLQSCSSK
VTEAFDYLSF LPLQTVQRLL KAVQPLLKVS MSMRDCLILV LRKAMFANQL DARKSAVAGF
LLLLKNFKVL GSLSSSQCSQ SLSVSQVHVD VHSHYNSVAN ETFCLEIMDS LRRCLSQQAD
VRLMLYEGFY DVLRRNSQLA NSVMQTLLSQ LKQFYEPKPD LLPPLKLEAC ILTQGDKISL
QEPLDYLLCC IQHCLAWYKN TVIPLQQGEE EEEEEEAFYE DLDDILESIT NRMIKSELED
FELDKSADFS QSTSIGIKNN ICAFLVMGVC EVLIEYNFSI SSFSKNRFED ILSLFMCYKK
LSDILNEKAG KAKTKMANKT SDSLLSM*

Position of stopcodon in wt / mu CDS

3807 / 2424

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

1269 / 808

Position of stopcodon in wt / mu cDNA

3911 / 2528

Position of start ATG in wt / mu cDNA

105 / 105

Last intron/exon boundary

3848

Theoretical NMD boundary in CDS

3693

Length of CDS

3807

Coding sequence (CDS) position

2422

cDNA position

2526

gDNA position

50019

Chromosomal position

89293963

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:

15:89293963A>T_5_ENST00000310775

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Known disease mutation: ClinVar ID 208639 (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

Chr15:89293963A>T (GRCh38)

Gene symbol

Gene constraints

LOEUF: 0.96, LOF (oe): 0.83, misssense (oe): 1.05, synonymous (oe): 1.06 ? (gnomAD)

Ensembl transcript ID

ENST00000310775.12

Genbank transcript ID

NM_001113378 (exact from MANE), NM_001376911 (by similarity)

UniProt / AlphaMissense peptide

FANCI_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.2422A>T
g.50019A>T

AA changes

K808* Score: 6.0?

Frameshift

No

Length of protein

NMD

Pathogenic variant (ClinVar)

Fanconi anemia complementation group I
Fanconi anemia

pathogenic

Variant DBs

dbSNP ID	rs375656231
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	0	63	63

Protein conservation

Species	Match	AA	Alignment
Human		808	A	N	K	T	S	D	S	L	L	S	M	K	F	V	S	S	L	L	T	A	L	F	R	D	S	I	Q	S	H	Q	E	S	L	S	V	L	R	S	S	N	E	F	M	R	Y	A	V	N	V	A	L	Q	K	V	Q	Q	L	K	E	T	G	H	V	S	G	P	D	G	Q	N	P	E	K	I	F	Q	N	L	C	D	I	T	R	V	L	L	W	R	Y	T	S	I	P	T	S	V	E	E	S	G	K	K	E	K	G	K	S	I	S	L	L	C	L	E	G	L	Q	K	I	F	S	A	V	Q	Q	F	Y	Q	P	K	I	Q	Q	F	L	R
mutated	no alignment	n/a
Ptroglodytes	all conserved	808	A	N	K	T	N	D	S	L	L	S	M	K	F	V	S	S	L	L	T	A	L	F	R	D	S	I	Q	S	H	Q	E	S	L	S	V	L	R	S	S	N	E	F	M	R	Y	A	V	N	V	A	L	Q	K	V	Q	Q	L	K	E	T	G	H	V	S	G	P	D	G	Q	N	P	D	K	I	F	Q	N	L	C	D	I	T	R	V	L	L	W	R	Y	T	S	I	P	T	S	V	E	E	S	G	K	K	E	K
Mmulatta	partly conserved	808	A	N	K	T	N	D	S	L	L	S	M	K	F	V	S	S	L	L	T	V	L	F	R	D	S	I	Q	S	H	Q	E	S	L	S	V	L	R	S	S	S	E	F	M	R	Y	A	V	N	I	A	L	Q	K	V	Q	Q	L	K	E	T	G	H	V	S	G	P	D	G	Q	N	P	D	K	I	F	Q	N	L	C	D	I	T	R	V	L	L	W	R	Y	T	S	I	P	T	S	V	E	E	L	G	K	K	E	K
Fcatus	partly conserved	802	A	N	K	T	N	D	S	F	L	S	M	K	F	V	S	D	L	L	T	A	L	F	R	D	S	A	Q	S	H	E	E	S	L	S	V	L	R	S	N	N	E	F	M	R	Y	A	V	S	V	A	L	Q	K	V	Q	Q	L	K	E	T	G	H	V	S	G	P	D	G	Q	N	P	E	K	I	F	Q	N	L	C	D	I	T	R	V	L	I	W	R	Y	T	S	I	P	T	S	V	E	D	S	G	K	K	E	K
Mmusculus	partly conserved	807	T	S	K	V	S	D	S	L	L	S	L	K	F	V	S	D	L	L	T	A	L	F	R	D	S	I	Q	S	H	E	E	S	L	S	V	L	R	S	S	G	E	F	M	H	Y	A	V	N	V	T	L	Q	K	I	Q	Q	L	I	R	T	G	H	V	S	G	P	D	G	Q	N	P	D	K	I	F	Q	N	L	C	D	I	T	R	V	L	L	W	R	Y	T	S	I	P	T	S	V	E	E	S	G	K	K	E	K
Ggallus	partly conserved	811	G	N	R	I	A	R	S	F	L	S	M	G	F	V	S	T	L	L	T	A	L	F	R	D	N	A	Q	S	H	E	E	S	L	A	V	L	R	S	S	T	E	F	M	R	Y	A	V	S	V	A	L	Q	K	V	Q	Q	L	E	E	M	G	Q	T	D	G	P	D	G	Q	N	P	E	K	M	F	Q	N	L	C	K	I	T	R	V	L	L	W	R	Y	T	S	I	P	T	A	V	E	E	P	G	K
Trubripes	partly conserved	810	S	H	K	T	P	R	S	L	L	S	M	G	F	I	S	T	L	L	T	L	L	F	R	D	S	T	Q	T	R	Q	E	A	L	S	V	L	R	S	N	G	E	F	V	R	Y	A	V	S	V	A	V	Q	K	I	Q	Q	L	E	E	T	G	H	T	D	G	P	D	G	Q	N	T	E	K	T	F	Q	F	L	C	D	M	T	S	V	L	M	W	R	Y	T	N	I	P	S	M	V	E	D	A	G	K
Drerio	no homologue
Dmelanogaster	partly conserved	809				KTMCTQ	P	D	N	I	W	D	L	A	I	L	D	K	L	L	H	L	L	L	D	D	V	V	AF	A	A	P	E	K	T	V	L	L	R	S	N	E	P	L	V	R	Y	V	L	S	V	T	A	S	R	V	E	S	I	R	-	-	-	-	-	L	E	P	D	Y	K	Q	L	A	Y	S	K	R	T	F	K	Q	L	T	D	I	T	K	V	I	-	-	-	Y	E	R	C	I	Q	R	L	P	E	L	W	K	N	F	D	M	Q	S	-	A	A	L	A	T	Q
Celegans	partly conserved	870						E	I	L	T	S	A	K	T	L	S	S	I	M	T	K	L	I	K
Xtropicalis	partly conserved	813	N	N	K	M	A	R	S	L	I	S	M	T	F	V	S	T	L	L	T	A	L	F	R	D	S	T	R	S	H	E	E	S	L	S	V	L	R	A	N	M	D	F	M	R	Y	S	V	C	V	A	L	Q	K	I	Q	Q	L	E	E	T	G	V	T	D	G	P	D	G	Q	N	S	E	K	M	F	Q	S	I	C	E	I	T	R	V	L	M	W	R	Y	N	S	I	P	T	A	A	E	N

Protein features

Start (aa)	End (aa)	Feature	Details
1	1328	CHAIN		lost
807	818	HELIX		lost
823	833	HELIX		lost
836	856	HELIX		lost
862	865	TURN		lost
867	887	HELIX		lost
897	900	HELIX		lost
904	922	HELIX		lost
924	926	HELIX		lost
927	932	HELIX		lost
951	970	HELIX		lost
952	952	MOD_RES	Phosphothreonine	lost
979	993	HELIX		lost
998	1000	STRAND		lost
1001	1016	HELIX		lost
1022	1037	HELIX		lost
1043	1057	HELIX		lost
1062	1064	STRAND		lost
1077	1083	TURN		lost
1084	1109	HELIX		lost
1121	1121	MOD_RES	Phosphoserine	lost
1128	1148	HELIX		lost
1157	1183	HELIX		lost
1184	1186	TURN		lost
1192	1204	HELIX		lost
1206	1218	HELIX		lost
1237	1245	HELIX		lost
1249	1271	HELIX		lost
1276	1278	TURN		lost
1284	1287	STRAND		lost
1293	1296	HELIX		lost
1300	1328	REGION		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	6.055	1
	4.55	1
(flanking)	4.724	1

?

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

15

Strand

1

Original gDNA sequence snippet

GTGATAGTCTTTTGTCCATGAAATTTGTGTCCAGTCTTCTC

Altered gDNA sequence snippet

GTGATAGTCTTTTGTCCATGTAATTTGTGTCCAGTCTTCTC

Original cDNA sequence snippet

GTGATAGTCTTTTGTCCATGAAATTTGTGTCCAGTCTTCTC

Altered cDNA sequence snippet

GTGATAGTCTTTTGTCCATGTAATTTGTGTCCAGTCTTCTC

Wildtype AA sequence

MDQKILSLAA EKTADKLQEF LQTLREGDLT NLLQNQAVKG KVAGALLRAI FKGSPCSEEA
GTLRRRKIYT CCIQLVESGD LQKEIASEII GLLMLEAHHF PGPLLVELAN EFISAVREGS
LVNGKSLELL PIILTALATK KENLAYGKGV LSGEECKKQL INTLCSGRWD QQYVIQLTSM
FKDVPLTAEE VEFVVEKALS MFSKMNLQEI PPLVYQLLVL SSKGSRKSVL EGIIAFFSAL
DKQHNEEQSG DELLDVVTVP SGELRHVEGT IILHIVFAIK LDYELGRELV KHLKVGQQGD
SNNNLSPFSI ALLLSVTRIQ RFQDQVLDLL KTSVVKSFKD LQLLQGSKFL QNLVPHRSYV
STMILEVVKN SVHSWDHVTQ GLVELGFILM DSYGPKKVLD GKTIETSPSL SRMPNQHACK
LGANILLETF KIHEMIRQEI LEQVLNRVVT RASSPISHFL DLLSNIVMYA PLVLQSCSSK
VTEAFDYLSF LPLQTVQRLL KAVQPLLKVS MSMRDCLILV LRKAMFANQL DARKSAVAGF
LLLLKNFKVL GSLSSSQCSQ SLSVSQVHVD VHSHYNSVAN ETFCLEIMDS LRRCLSQQAD
VRLMLYEGFY DVLRRNSQLA NSVMQTLLSQ LKQFYEPKPD LLPPLKLEAC ILTQGDKISL
QEPLDYLLCC IQHCLAWYKN TVIPLQQGEE EEEEEEAFYE DLDDILESIT NRMIKSELED
FELDKSADFS QSTSIGIKNN ICAFLVMGVC EVLIEYNFSI SSFSKNRFED ILSLFMCYKK
LSDILNEKAG KAKTKMANKT SDSLLSMKFV SSLLTALFRD SIQSHQESLS VLRSSNEFMR
YAVNVALQKV QQLKETGHVS GPDGQNPEKI FQNLCDITRV LLWRYTSIPT SVEESGKKEK
GKSISLLCLE GLQKIFSAVQ QFYQPKIQQF LRALDVTDKE GEEREDADVS VTQRTAFQIR
QFQRSLLNLL SSQEEDFNSK EALLLVTVLT SLSKLLEPSS PQFVQMLSWT SKICKENSRE
DALFCKSLMN LLFSLHVSYK SPVILLRDLS QDIHGHLGDI DQDVEVEKTN HFAIVNLRTA
APTVCLLVLS QAEKVLEEVD WLITKLKGQV SQETLSEEAS SQATLPNQPV EKAIIMQLGT
LLTFFHELVQ TALPSGSCVD TLLKDLCKMY TTLTALVRYY LQVCQSSGGI PKNMEKLVKL
SGSHLTPLCY SFISYVQNKS KSLNYTGEKK EKPAAVATAM ARVLRETKPI PNLIFAIEQY
EKFLIHLSKK SKVNLMQHMK LSTSRDFKIK GNILDMVLRE DGEDENEEGT ASEHGGQNKE
PAKKKRKK*

Mutated AA sequence

MDQKILSLAA EKTADKLQEF LQTLREGDLT NLLQNQAVKG KVAGALLRAI FKGSPCSEEA
GTLRRRKIYT CCIQLVESGD LQKEIASEII GLLMLEAHHF PGPLLVELAN EFISAVREGS
LVNGKSLELL PIILTALATK KENLAYGKGV LSGEECKKQL INTLCSGRWD QQYVIQLTSM
FKDVPLTAEE VEFVVEKALS MFSKMNLQEI PPLVYQLLVL SSKGSRKSVL EGIIAFFSAL
DKQHNEEQSG DELLDVVTVP SGELRHVEGT IILHIVFAIK LDYELGRELV KHLKVGQQGD
SNNNLSPFSI ALLLSVTRIQ RFQDQVLDLL KTSVVKSFKD LQLLQGSKFL QNLVPHRSYV
STMILEVVKN SVHSWDHVTQ GLVELGFILM DSYGPKKVLD GKTIETSPSL SRMPNQHACK
LGANILLETF KIHEMIRQEI LEQVLNRVVT RASSPISHFL DLLSNIVMYA PLVLQSCSSK
VTEAFDYLSF LPLQTVQRLL KAVQPLLKVS MSMRDCLILV LRKAMFANQL DARKSAVAGF
LLLLKNFKVL GSLSSSQCSQ SLSVSQVHVD VHSHYNSVAN ETFCLEIMDS LRRCLSQQAD
VRLMLYEGFY DVLRRNSQLA NSVMQTLLSQ LKQFYEPKPD LLPPLKLEAC ILTQGDKISL
QEPLDYLLCC IQHCLAWYKN TVIPLQQGEE EEEEEEAFYE DLDDILESIT NRMIKSELED
FELDKSADFS QSTSIGIKNN ICAFLVMGVC EVLIEYNFSI SSFSKNRFED ILSLFMCYKK
LSDILNEKAG KAKTKMANKT SDSLLSM*

Position of stopcodon in wt / mu CDS

3987 / 2424

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

1329 / 808

Position of stopcodon in wt / mu cDNA

4061 / 2498

Position of start ATG in wt / mu cDNA

75 / 75

Last intron/exon boundary

3998

Theoretical NMD boundary in CDS

3873

Length of CDS

3987

Coding sequence (CDS) position

2422

cDNA position

2496

gDNA position

50019

Chromosomal position

89293963

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