Is STRA6 p.Val12Asp (c.35T>A) pathogenic?

STRA6 p.Val12Asp (c.35T>A) is classified Uncertain significance in STRA6 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-07-06). Ultra-rare (popmax 0.011%, afr); Associated with Inborn genetic diseases.

What condition is associated with STRA6 p.Val12Asp (c.35T>A)?

STRA6 p.Val12Asp (c.35T>A) is associated with Inborn genetic diseases (ClinVar).

How common is STRA6 p.Val12Asp (c.35T>A) in the general population?

STRA6 p.Val12Asp (c.35T>A) is ultra-rare (popmax 0.011%, afr) (gnomAD).

STRA6 p.Val12Asp

c.35T>A · rs978665180 · VCV2234628

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.011%, afr)

Conditions

Inborn genetic diseases

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.226	benign-leaning
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 0.037	GERP -4.4
Overall
CADD	5.511	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.011% African / African-American · 8/73,012 alleles

Filtering AF 0.0054% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00389%

Overall 0.000782% 12/1,535,488 alleles · ultra-rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.011%	9,127
Remaining individualsnot grpmax-eligible	0.00167%	59,992
European (non-Finnish)	0.000262%	382,297

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: STRA6
Protein: p.Val12Asp
Coding: c.35T>A
MANE Select: NM_022369 · reported on NM_001199040
dbSNP: rs978665180
Type: single nucleotide variant
Location: chr15:74209420 (GRCh38)

Full STRA6 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

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/stra6-p-val12asp (accessed [today's date]).

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