MutationT@ster 2025

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Querying Taster for transcript #1: ENST00000262613
MT speed 0.35 s - this script 2.825209 s

Transcript summary:

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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
ENST00000262613(MANE Select)	NHERF1	Benign	42\|58	simple_aae		No				Single base exchange		Normal	Amino acid sequence changed Homozygous in gnomAD Protein features (might be) affected

MutationT@ster 2025

Variant:

17:74749174C>G_1_ENST00000262613

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Prediction:

BenignPermalink

Summary:

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

Model: simple_aae
Tree vote: 42|58 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr17:74749174C>G (GRCh38)

Gene symbol

NHERF1

Gene constraints

LOEUF: 1.33, LOF (oe): 0.94, misssense (oe): 1.11, synonymous (oe): 1.10 ? (gnomAD)

Ensembl transcript ID

ENST00000262613.10

Genbank transcript ID

NM_004252 (exact from MANE)

UniProt / AlphaMissense peptide

NHRF1_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.328C>G
g.547C>G

AA changes

AAE:	L110V	?
Score:	32

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs35910969
gnomAD	homozygous (G/G)	heterozygous	allele carriers
	619	>32000	>32000

Protein conservation

Species	Match	AA	Alignment
Human		110	L	Q	K	L	G	V	Q	V	R	E	E	L	L	R	A	Q	E	A	P	G	Q	A	E	P
mutated	all conserved	110	L	Q	K	L	G	V	Q	V	R	E	E	V	L	R	A	Q	E	A	P	G	Q	A
Ptroglodytes	all identical	110	L	Q	K	L	G	V	Q	V	R	E	E	L	L	R	A	Q	E	A	P	G	Q	A
Mmulatta	all identical	110	L	Q	K	L	G	V	Q	V	R	E	E	L	L	R	A	Q	E	T	P	G	Q	A
Fcatus	all identical	110	L	Q	K	L	G	V	Q	V	R	E	E	L	L	R	A	Q	D	G	P	G	Q	A
Mmusculus	all identical	110	L	K	K	L	G	V	S	I	R	E	E	L	L	R	P	Q	E	K	S	E	Q	A
Ggallus	not conserved	109	P	P	K	T	H	S	D	-	-	-	-	-	-	-	-	P	D	G	E	A	Q	R	E
Trubripes	not conserved	108	L	K	K	H	N	L	K	C	A	P	E	F	V	TDGLPIPFDDGEAEVEVEEE
Drerio	no homologue
Dmelanogaster	not conserved	120	-	-	-	-	-	-	-	-	-	-	-	-	-	K	A	L	E	V	K	P	A	S	P
Celegans	no homologue
Xtropicalis	all conserved	102	-	-	-	-	-	-	-	V	E	E	E	V	A	-	-	-	-	-	-	-	-	-	-

Protein features

Start (aa)	End (aa)	Feature	Details
2	358	CHAIN		lost
109	112	HELIX		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	1.001	0.924
	-0.095	0.435
(flanking)	1.027	0.901

?

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

17

Strand

1

Original gDNA sequence snippet

GCGTCCAGGTCCGAGAGGAGCTGCTGCGCGCCCAGGAAGCG

Altered gDNA sequence snippet

GCGTCCAGGTCCGAGAGGAGGTGCTGCGCGCCCAGGAAGCG

Original cDNA sequence snippet

GCGTCCAGGTCCGAGAGGAGCTGCTGCGCGCCCAGGAAGCG

Altered cDNA sequence snippet

GCGTCCAGGTCCGAGAGGAGGTGCTGCGCGCCCAGGAAGCG

Wildtype AA sequence

MSADAAAGAP LPRLCCLEKG PNGYGFHLHG EKGKLGQYIR LVEPGSPAEK AGLLAGDRLV
EVNGENVEKE THQQVVSRIR AALNAVRLLV VDPETDEQLQ KLGVQVREEL LRAQEAPGQA
EPPAAAEVQG AGNENEPREA DKSHPEQREL RPRLCTMKKG PSGYGFNLHS DKSKPGQFIR
SVDPDSPAEA SGLRAQDRIV EVNGVCMEGK QHGDVVSAIR AGGDETKLLV VDRETDEFFK
KCRVIPSQEH LNGPLPVPFT NGEIQKENSR EALAEAALES PRPALVRSAS SDTSEELNSQ
DSPPKQDSTA PSSTSSSDPI LDFNISLAMA KERAHQKRSS KRAPQMDWSK KNELFSNL*

Mutated AA sequence

MSADAAAGAP LPRLCCLEKG PNGYGFHLHG EKGKLGQYIR LVEPGSPAEK AGLLAGDRLV
EVNGENVEKE THQQVVSRIR AALNAVRLLV VDPETDEQLQ KLGVQVREEV LRAQEAPGQA
EPPAAAEVQG AGNENEPREA DKSHPEQREL RPRLCTMKKG PSGYGFNLHS DKSKPGQFIR
SVDPDSPAEA SGLRAQDRIV EVNGVCMEGK QHGDVVSAIR AGGDETKLLV VDRETDEFFK
KCRVIPSQEH LNGPLPVPFT NGEIQKENSR EALAEAALES PRPALVRSAS SDTSEELNSQ
DSPPKQDSTA PSSTSSSDPI LDFNISLAMA KERAHQKRSS KRAPQMDWSK KNELFSNL*

Position of stopcodon in wt / mu CDS

1077 / 1077

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

359 / 359

Position of stopcodon in wt / mu cDNA

1296 / 1296

Position of start ATG in wt / mu cDNA

220 / 220

Last intron/exon boundary

1107

Theoretical NMD boundary in CDS

837

Length of CDS

1077

Coding sequence (CDS) position

328

cDNA position

547

gDNA position

547

Chromosomal position

74749174

Speed

0.35 s

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

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