Is TAF1 p.Met1426Val (c.4276A>G) pathogenic?

TAF1 p.Met1426Val (c.4276A>G) is classified Likely pathogenic in TAF1 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-04-26). AlphaMissense: ambiguous (0.3959); Absent from gnomAD v4.1.

How common is TAF1 p.Met1426Val (c.4276A>G) in the general population?

TAF1 p.Met1426Val (c.4276A>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about TAF1 p.Met1426Val (c.4276A>G)?

AlphaMissense predicts ambiguous (score 0.3959) — an in-silico prediction, not a clinical call.

TAF1 p.Met1426Val

c.4276A>G · rs2148488085 · VCV1098389

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.3959 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Computational evidence

Protein change
AlphaMissense	0.3959	ambiguous
REVEL	0.436	indeterminate
SaProt	—	not scored · why
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 11	GERP 1.7, phastCons 1
Regional constraint	o/e 0.39	unconstrained · MANE · 17 kb · p 4.2e-15 · regional, not allelic
Overall
CADD	24.6	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL is an independent agreement signal.

⚠ Isoform check: AlphaMissense numbered on a different transcript (AM M1425V vs ClinVar M1426V) — verify the residue.

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: TAF1
Protein: p.Met1426Val
Coding: c.4276A>G
MANE Select: NM_004606
dbSNP: rs2148488085
Type: single nucleotide variant
Location: chrX:71408043 (GRCh38)
Structure: AlphaFold pLDDT 62.62 · 65 PDB

Full TAF1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

TAF1 p.Arg1062Cys Likely pathogenic ★★ ⚠ same type
TAF1 p.Arg1234Gln Pathogenic/Likely pathogenic ★★ same type
TAF1 p.Arg1432His Pathogenic ★★ same type
TAF1 p.Arg870Cys Pathogenic/Likely pathogenic ★★ same type
TAF1 p.Asn1497His Pathogenic/Likely pathogenic ★★ same type
TAF1 p.Ile1317Thr Pathogenic ★★ same type
TAF1 p.Phe403Val Pathogenic/Likely pathogenic ★★ same type
TAF1 c.1774-3T>C Uncertain significance ★★ same type

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/taf1-p-met1426val (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown