Is TEX264 p.Leu7Val (c.19C>G) pathogenic?

TEX264 p.Leu7Val (c.19C>G) is classified Uncertain significance in TEX264 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-04-30). AlphaMissense: likely benign (0.1203); Very rare (popmax 0.00768%, sas).

How common is TEX264 p.Leu7Val (c.19C>G) in the general population?

TEX264 p.Leu7Val (c.19C>G) is very rare (popmax 0.00768%, sas) (gnomAD).

What do computational predictors say about TEX264 p.Leu7Val (c.19C>G)?

AlphaMissense predicts likely benign (score 0.1203) — an in-silico prediction, not a clinical call.

TEX264 p.Leu7Val

c.19C>G · VCV3967853

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1203 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00768%, sas)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1203	likely benign
REVEL	0.123	moderately benign-leaning
SaProt	LLR -7.38	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 4.9	GERP 0.25, phastCons 1
Regional constraint	o/e 0.84	unconstrained · MANE · 30 kb · p 0.00092 · regional, not allelic
Overall
CADD	19.0	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00768% South Asian · 7/91,090 alleles

Filtering AF 0.00359% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00255%

Overall 0.000434% 7/1,614,224 alleles · very rare exomes 7/1,461,888 · genomes 0/152,336 · joint denominator

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: TEX264
Protein: p.Leu7Val
Coding: c.19C>G
MANE Select: NM_015926
Type: single nucleotide variant
Location: chr3:51674323 (GRCh38)
Gene constraint: LOEUF 0.798 · pLI 0.02 (gnomAD)
Structure: AlphaFold pLDDT 76.05 · 2 PDB

Full TEX264 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

TEX264 p.Ala127Ser Uncertain significance ★★ ⚠ same type
TEX264 p.Ala208Thr Uncertain significance ★ ⚠ same type
TEX264 p.Ala25Thr Uncertain significance ★ ⚠ same type
TEX264 p.Ala78Thr Uncertain significance ★ same type
TEX264 p.Ala95Ser Uncertain significance ★ ⚠ same type
TEX264 p.Arg162Gln Uncertain significance ★ ⚠ same type
TEX264 p.Arg162Trp Uncertain significance ★ ⚠ same type
TEX264 p.Arg186Gln 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/tex264-p-leu7val (accessed [today's date]).

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