Is STRA6 p.Ile342= (c.1026C>T) pathogenic?

STRA6 p.Ile342= (c.1026C>T) is classified Benign/Likely benign in STRA6 (ClinVar, Multiple submitters, 4 submitters; last evaluated 2024-07-19). Rare (popmax 0.48%, afr); Associated with microphthalmia, syndromic 9.

What condition is associated with STRA6 p.Ile342= (c.1026C>T)?

STRA6 p.Ile342= (c.1026C>T) is associated with microphthalmia, syndromic 9 (ClinVar).

How common is STRA6 p.Ile342= (c.1026C>T) in the general population?

STRA6 p.Ile342= (c.1026C>T) is rare (popmax 0.48%, afr) (gnomAD).

STRA6 p.Ile342=

c.1026C>T · rs79382990 · VCV772409

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

gnomAD v4.1

Rare

rare (popmax 0.48%, afr)

Conditions

microphthalmia, syndromic 9

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.19	GERP -3.9
Overall
CADD	7.261	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.48% African / African-American · 360/75,038 alleles

Filtering AF 0.439% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.423%

Overall 0.0384% 619/1,614,078 alleles · rare exomes 387/1,461,752 · genomes 232/152,326 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.48%	208
Remaining individualsnot grpmax-eligible	0.0624%	1,603
Admixed American	0.0417%	2,401
Middle Eastern	0.033%	3,031
European (non-Finnish)	0.0158%	6,310
East Asian	0.00891%	11,222
South Asian	0.0022%	45,516

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.Ile342=
Coding: c.1026C>T
MANE Select: NM_022369
dbSNP: rs79382990
Type: single nucleotide variant
Location: chr15:74189179 (GRCh38)
Gene constraint: LOEUF 0.725 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 78.18

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

Disease context

microphthalmia, syndromic 9 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

STRA6 p.Ile342Met Uncertain significance ★ ⚠ same residue
STRA6 c.267-1G>T Pathogenic/Likely pathogenic ★★ same condition
STRA6 p.Arg532Ter Pathogenic ★★ same condition
STRA6 p.Thr644Met Pathogenic ★★ ⚠ same condition
STRA6 c.*10A>C Uncertain significance ★★ same condition
STRA6 p.Ala54Ser Uncertain significance ★★ ⚠ same condition
STRA6 p.Ala557Val Uncertain significance ★★ ⚠ same condition
STRA6 p.Arg467Cys Uncertain significance ★★ ⚠ same condition

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-ile342 (accessed [today's date]).

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