STRA6

Chr 15

signaling receptor and transporter of retinol STRA6

Also known as: MCOPCB8, MCOPS9, PP14296, SLC69A1

NCBI Gene: 64220 ENSG00000137868 UniProt: Q9BX79

The protein encoded by this gene is a membrane protein involved in the metabolism of retinol. The encoded protein acts as a receptor for retinol/retinol binding protein complexes. This protein removes the retinol from the complex and transports it across the cell membrane. Defects in this gene are a cause of syndromic microphthalmia type 9 (MCOPS9). Several transcript variants encoding a few different isoforms have been found for this gene. [provided by RefSeq, Dec 2008]

Research

ResearchGenerating clinical summary…

Primary Disease Associations & Inheritance

UniProtMicrophthalmia, syndromic, 9

Clinical highlights

Interpreting a novel variant

Loss of function is the curated mechanism (Gene2Phenotype), though the gene is not strongly LoF-constrained in the population — weigh truncating variants against that tolerance.Curated gene-level mechanism — a prior for triage, not a per-variant call.

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

0.82

LOEUF

LOF

Mechanism· G2P

Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

0.82LOEUF

pLI 0.000

Z-score 2.42

OE 0.58 (0.41–0.82)

Tolerant

Typical tolerance to LoF variation

Missense Constraint?

0.60Z-score

OE missense 0.91 (0.84–1.00)

355 obs / 388.2 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.58 (0.41–0.82)

0≤0.351.4

Missense OE?0.91 (0.84–1.00)

0≤0.61.4

Synonymous OE?1.12

0≤1.21.6

LoF obs/exp: 22 / 38.1Missense obs/exp: 355 / 388.2Syn Z: -1.19

Background carrier burden — how many people carry a rare variant somewhere in STRA6?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 36

928 rare PASS variants

Rare truncating (LoF)

1 in 670

164 rare PASS variants

Rare synonymous (reference)

1 in 75

414 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for STRA6. A background rate for each class, not the frequency of any particular variant; thin-coverage exons undercount.

By genetic ancestry · 9 gnomAD groups · rare = under 0.1% in that group

Group	People	Missense	Truncating
European (non-Finnish)	~556k	1 in 53	1 in 740
South Asian	~43k	1 in 61	1 in 2,000
Remaining (unassigned)	~30k	1 in 40	1 in 1,300
European (Finnish)	~27k	1 in 140	1 in 2,600
Admixed American	~22k	1 in 51	1 in 1,200
African / African American	~21k	1 in 49	1 in 630
East Asian	~20k	1 in 63	1 in 1,400
Ashkenazi Jewish	~13k	1 in 180	≈ 1 in 13,000
Middle Eastern	~2,884	1 in 55	≈ 1 in 1,400

Each group is summed over the variants that are rare in that group. Grey ≈ figures rest on fewer than five expected carriers — too few to distinguish groups. Differences mostly reflect how many people were sampled and how much variation each ancestry carries, not disease risk.

Exome coverage (gnomAD): 16 of 18 coding exons well covered in gnomAD exomes; exon 6 poorly covered; exon 2 marginal. Genomes: all 18.? see exons ↓