Is ASB11 p.Val41Ile (c.121G>A) pathogenic?

ASB11 p.Val41Ile (c.121G>A) is classified Uncertain significance in ASB11 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-08-12). AlphaMissense: likely benign (0.2099); Rare (popmax 0.194%, sas).

How common is ASB11 p.Val41Ile (c.121G>A) in the general population?

ASB11 p.Val41Ile (c.121G>A) is rare (popmax 0.194%, sas) (gnomAD).

What do computational predictors say about ASB11 p.Val41Ile (c.121G>A)?

AlphaMissense predicts likely benign (score 0.2099) — an in-silico prediction, not a clinical call.

ASB11 p.Val41Ile

c.121G>A · rs781653107 · VCV3130088

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.2099 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.194%, sas)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.2099	likely benign
REVEL	0.173	moderately benign-leaning
SaProt	LLR -5.80	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 4.8	GERP 1.8, phastCons 1
Regional constraint	o/e 1.01	unconstrained · MANE · 32 kb · p 0.9 · regional, not allelic
Overall
CADD	20.2	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 0.194% South Asian · 93/47,818 alleles

Filtering AF 0.162% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.151%

Overall 0.00867% 101/1,165,343 alleles · rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.194%	514
Remaining individualsnot grpmax-eligible	0.00882%	11,340
European (non-Finnish)	0.000457%	219,023

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: ASB11
Protein: p.Val41Ile
Coding: c.121G>A
MANE Select: NM_080873
dbSNP: rs781653107
Type: single nucleotide variant
Location: chrX:15315485 (GRCh38)
Structure: AlphaFold pLDDT 87.28 · 1 PDB

Full ASB11 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

ASB11 p.Arg256His Uncertain significance ★★ ⚠ same type
ASB11 p.Arg208Trp Benign ★★ ⚠ same type
ASB11 p.Asp249Asn Benign ★★ ⚠ same type
ASB11 p.Ala114Gly Uncertain significance ★ ⚠ same type
ASB11 p.Ala145Thr Uncertain significance ★ ⚠ same type
ASB11 p.Ala259Gly Uncertain significance ★ ⚠ same type
ASB11 p.Ala268Val Uncertain significance ★ ⚠ same type
ASB11 p.Arg281Cys 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/asb11-p-val41ile (accessed [today's date]).

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