Is STRA6 p.Pro667= (c.2001C>T) pathogenic?

STRA6 p.Pro667= (c.2001C>T) is classified Likely benign in STRA6 (ClinVar, Single submitter, 1 submitter; last evaluated 2019-04-24). Ultra-rare (popmax 0.0331%, mid); Associated with microphthalmia, syndromic 9.

What condition is associated with STRA6 p.Pro667= (c.2001C>T)?

STRA6 p.Pro667= (c.2001C>T) is associated with microphthalmia, syndromic 9 (ClinVar).

How common is STRA6 p.Pro667= (c.2001C>T) in the general population?

STRA6 p.Pro667= (c.2001C>T) is ultra-rare (popmax 0.0331%, mid) (gnomAD).

STRA6 p.Pro667=

c.2001C>T · rs147077716 · VCV464033

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0331%, mid)

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 5.8	GERP 0.86, phastCons 1
Overall
CADD	9.296	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0331% Middle Eastern · 2/6,050 alleles

Filtering AF 0.0301% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.029%

Overall 0.0287% 463/1,612,998 alleles · ultra-rare exomes 430/1,460,642 · genomes 33/152,356 · joint denominator

Ancestry group	Frequency	1 in
Remaining individualsnot grpmax-eligible	0.0544%	1,837
Finnishnot grpmax-eligible	0.0344%	2,904
Middle Easterngrpmax	0.0331%	3,025
European (non-Finnish)	0.0328%	3,047
Admixed American	0.015%	6,667
South Asian	0.00879%	11,379
African / African-American	0.00133%	75,042

Remaining individuals shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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.Pro667=
Coding: c.2001C>T
MANE Select: NM_022369
dbSNP: rs147077716
Type: single nucleotide variant
Location: chr15:74180083 (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 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
STRA6 p.Arg655Cys 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-pro667 (accessed [today's date]).

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