MutationT@ster 2025

NEVER press reload or F5 - unless you want to start from the very beginning.
Input seems to be ok - now mapping the variant to the different transcripts...
Querying Taster for transcript #1: ENST00000260956
Querying Taster for transcript #2: ENST00000409333
MT speed 3.39 s - this script 5.844859 s

Transcript summary:

Permalink

Transcript	Gene symbol	Prediction	Tree vote	Model	Prediction problem	Splice site change	Known ClinVar disease mutation	Potential ClinVar disease mutation	Amino acid changes	Variant type	dbSNP ID	Protein length	Features at a glance
ENST00000409333	SSB	Deleterious	53\|47	simple_aae		No				Single base exchange		Normal	Amino acid sequence changed Protein features (might be) affected
ENST00000260956(MANE Select)	SSB	Benign	43\|57	simple_aae		No				Single base exchange		Normal	Amino acid sequence changed Protein features (might be) affected

MutationT@ster 2025

Variant:

2:169805774A>G_2_ENST00000409333

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected

Model: simple_aae
Tree vote: 53|47 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr2:169805774A>G (GRCh38)

Gene symbol

SSB

Gene constraints

LOEUF: 0.41, LOF (oe): 0.24, misssense (oe): 0.64, synonymous (oe): 0.69 ? (gnomAD)

Ensembl transcript ID

ENST00000409333.1

Genbank transcript ID

NM_001294145 (by similarity)

UniProt / AlphaMissense peptide

LA_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.280A>G
g.13842A>G

AA changes

AAE:	S94G	?
Score:	56

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs751375349
gnomAD	homozygous (G/G)	heterozygous	allele carriers
	0	1	1

Protein conservation

Species	Match	AA	Alignment
Human		94	S	E	D	K	T	K	I	R	R	S	P	S	K	P	L	P	E	V	T	D	E	Y	K	N
mutated	not conserved	94	S	E	D	K	T	K	I	R	R	S	P	G	K	P	L	P	E	V	T	D	E	Y	K
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	408	CHAIN		lost
7	99	DOMAIN	HTH La-type RNA-binding	lost
94	94	MOD_RES	Phosphoserine	lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	3.99	1
	4.173	1
(flanking)	0.695	0.993

?

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

2

Strand

1

Original gDNA sequence snippet

CTAAAATCAGAAGGTCTCCAAGCAAACCCCTACCTGAAGTG

Altered gDNA sequence snippet

CTAAAATCAGAAGGTCTCCAGGCAAACCCCTACCTGAAGTG

Original cDNA sequence snippet

CTAAAATCAGAAGGTCTCCAAGCAAACCCCTACCTGAAGTG

Altered cDNA sequence snippet

CTAAAATCAGAAGGTCTCCAGGCAAACCCCTACCTGAAGTG

Wildtype AA sequence

MAENGDNEKM AALEAKICHQ IEYYFGDFNL PRDKFLKEQI KLDEGWVPLE IMIKFNRLNR
LTTDFNVIVE ALSKSKAELM EISEDKTKIR RSPSKPLPEV TDEYKNDVKN RSVYIKGFPT
DATLDDIKEW LEDKGQVLNI QMRRTLHKAF KGSIFVVFDS IESAKKFVET PGQKYKETDL
LILFKDDYFA KKNEERKQNK VEAKLRAKQE QEAKQKLEED AEMKSLEEKI GCLLKFSGDL
DDQTCREDLH ILFSNHGEIK WIDFVRGAKE GIILFKEKAK EALGKAKDAN NGNLQLRNKE
VTWEVLEGEV EKEALKKIIE DQQESLNKWK SKGRRFKGKG KGNKAAQPGS GKGKVQFQGK
KTKFASDDEH DEHDENGATG PVKRAREETD KEEPASKQQK TENGAGDQ*

Mutated AA sequence

MAENGDNEKM AALEAKICHQ IEYYFGDFNL PRDKFLKEQI KLDEGWVPLE IMIKFNRLNR
LTTDFNVIVE ALSKSKAELM EISEDKTKIR RSPGKPLPEV TDEYKNDVKN RSVYIKGFPT
DATLDDIKEW LEDKGQVLNI QMRRTLHKAF KGSIFVVFDS IESAKKFVET PGQKYKETDL
LILFKDDYFA KKNEERKQNK VEAKLRAKQE QEAKQKLEED AEMKSLEEKI GCLLKFSGDL
DDQTCREDLH ILFSNHGEIK WIDFVRGAKE GIILFKEKAK EALGKAKDAN NGNLQLRNKE
VTWEVLEGEV EKEALKKIIE DQQESLNKWK SKGRRFKGKG KGNKAAQPGS GKGKVQFQGK
KTKFASDDEH DEHDENGATG PVKRAREETD KEEPASKQQK TENGAGDQ*

Position of stopcodon in wt / mu CDS

1227 / 1227

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

409 / 409

Position of stopcodon in wt / mu cDNA

1474 / 1474

Position of start ATG in wt / mu cDNA

248 / 248

Last intron/exon boundary

1385

Theoretical NMD boundary in CDS

1087

Length of CDS

1227

Coding sequence (CDS) position

280

cDNA position

527

gDNA position

13842

Chromosomal position

169805774

Speed

3.19 s

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

Back to summary table

MutationT@ster 2025

Variant:

2:169805774A>G_1_ENST00000260956

Back to summary table

Prediction:

BenignPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected

Model: simple_aae
Tree vote: 43|57 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr2:169805774A>G (GRCh38)

Gene symbol

SSB

Gene constraints

LOEUF: 0.41, LOF (oe): 0.24, misssense (oe): 0.64, synonymous (oe): 0.69 ? (gnomAD)

Ensembl transcript ID

ENST00000260956.9

Genbank transcript ID

NM_003142 (exact from MANE)

UniProt / AlphaMissense peptide

LA_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.280A>G
g.13842A>G

AA changes

AAE:	S94G	?
Score:	56

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs751375349
gnomAD	homozygous (G/G)	heterozygous	allele carriers
	0	1	1

Protein conservation

Species	Match	AA	Alignment
Human		94	S	E	D	K	T	K	I	R	R	S	P	S	K	P	L	P	E	V	T	D	E	Y	K	N
mutated	not conserved	94	S	E	D	K	T	K	I	R	R	S	P	G	K	P	L	P	E	V	T	D	E	Y	K
Ptroglodytes	all identical	94	S	E	D	K	T	K	I	R	R	S	P	S	K	P	L	P	E	V	T	D	E	Y	K
Mmulatta	no homologue
Fcatus	all identical	94	S	E	D	K	T	K	I	R	R	S	P	S	K	P	L	P	E	V	T	D	E	Y	K
Mmusculus	all identical	94	S	A	D	K	T	K	I	R	R	S	P	S	R	P	L	P	E	V	T	D	E	Y	K
Ggallus	all conserved	94	N	E	D	K	T	K	I	R	R	S	P	N	K	P	L	P	E	L	N	D	Q	Y	K
Trubripes	not conserved	92	S	E	D	K	T	K	I	R	R	S	L	D	K	P	L	P	E	I	N	D	D	Y	K
Drerio	no homologue
Dmelanogaster	not conserved	132	S	E	D	K	L	S	L	R	R	H	P	E	R	P	I	P	E	H	N	E	E	R	R
Celegans	not conserved	93	S	E	D	N	Q	K	I	R	R	N	E	E	N	P	V	P	E	N	S	L	E	Y	W
Xtropicalis	all conserved	94	D	E	D	K	C	K	I	R	R	S	P	A	K	P	L	P	E	L	N	D	E	Y	K

Protein features

Start (aa)	End (aa)	Feature	Details
1	408	CHAIN		lost
7	99	DOMAIN	HTH La-type RNA-binding	lost
94	94	MOD_RES	Phosphoserine	lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	3.99	1
	4.173	1
(flanking)	0.695	0.993

?

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

2

Strand

1

Original gDNA sequence snippet

CTAAAATCAGAAGGTCTCCAAGCAAACCCCTACCTGAAGTG

Altered gDNA sequence snippet

CTAAAATCAGAAGGTCTCCAGGCAAACCCCTACCTGAAGTG

Original cDNA sequence snippet

CTAAAATCAGAAGGTCTCCAAGCAAACCCCTACCTGAAGTG

Altered cDNA sequence snippet

CTAAAATCAGAAGGTCTCCAGGCAAACCCCTACCTGAAGTG

Wildtype AA sequence

MAENGDNEKM AALEAKICHQ IEYYFGDFNL PRDKFLKEQI KLDEGWVPLE IMIKFNRLNR
LTTDFNVIVE ALSKSKAELM EISEDKTKIR RSPSKPLPEV TDEYKNDVKN RSVYIKGFPT
DATLDDIKEW LEDKGQVLNI QMRRTLHKAF KGSIFVVFDS IESAKKFVET PGQKYKETDL
LILFKDDYFA KKNEERKQNK VEAKLRAKQE QEAKQKLEED AEMKSLEEKI GCLLKFSGDL
DDQTCREDLH ILFSNHGEIK WIDFVRGAKE GIILFKEKAK EALGKAKDAN NGNLQLRNKE
VTWEVLEGEV EKEALKKIIE DQQESLNKWK SKGRRFKGKG KGNKAAQPGS GKGKVQFQGK
KTKFASDDEH DEHDENGATG PVKRAREETD KEEPASKQQK TENGAGDQ*

Mutated AA sequence

MAENGDNEKM AALEAKICHQ IEYYFGDFNL PRDKFLKEQI KLDEGWVPLE IMIKFNRLNR
LTTDFNVIVE ALSKSKAELM EISEDKTKIR RSPGKPLPEV TDEYKNDVKN RSVYIKGFPT
DATLDDIKEW LEDKGQVLNI QMRRTLHKAF KGSIFVVFDS IESAKKFVET PGQKYKETDL
LILFKDDYFA KKNEERKQNK VEAKLRAKQE QEAKQKLEED AEMKSLEEKI GCLLKFSGDL
DDQTCREDLH ILFSNHGEIK WIDFVRGAKE GIILFKEKAK EALGKAKDAN NGNLQLRNKE
VTWEVLEGEV EKEALKKIIE DQQESLNKWK SKGRRFKGKG KGNKAAQPGS GKGKVQFQGK
KTKFASDDEH DEHDENGATG PVKRAREETD KEEPASKQQK TENGAGDQ*

Position of stopcodon in wt / mu CDS

1227 / 1227

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

409 / 409

Position of stopcodon in wt / mu cDNA

1342 / 1342

Position of start ATG in wt / mu cDNA

116 / 116

Last intron/exon boundary

1253

Theoretical NMD boundary in CDS

1087

Length of CDS

1227

Coding sequence (CDS) position

280

cDNA position

395

gDNA position

13842

Chromosomal position

169805774

Speed

0.20 s

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

Back to summary table