RARRES1

Chr 3

retinoic acid receptor responder 1

Also known as: LXNL, PERG-1, TIG1

NCBI Gene: 5918 ENSG00000118849 UniProt: P49788 OMIM: 605090

This gene was identified as a retinoid acid (RA) receptor-responsive gene. It encodes a type 1 membrane protein. The expression of this gene is upregulated by tazarotene as well as by retinoic acid receptors. The expression of this gene is found to be downregulated in prostate cancer, which is caused by the methylation of its promoter and CpG island. Alternatively spliced transcript variant encoding distinct isoforms have been observed. [provided by RefSeq, Jul 2008]

OMIM Research

OMIM ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

1.61

LOEUF

—

Mechanism

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.61LOEUF

pLI 0.000

Z-score -0.08

OE 1.02 (0.67–1.61)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

0.82Z-score

OE missense 0.79 (0.67–0.94)

98 obs / 123.8 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?1.02 (0.67–1.61)

0≤0.351.4

Missense OE?0.79 (0.67–0.94)

0≤0.61.4

Synonymous OE?0.83

0≤1.21.6

LoF obs/exp: 13 / 12.7Missense obs/exp: 98 / 123.8Syn Z: 0.88

Background carrier burden — how many people carry a rare variant somewhere in RARRES1?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 130

414 rare PASS variants

Rare truncating (LoF)

1 in 400

108 rare PASS variants

Rare synonymous (reference)

1 in 160

166 rare PASS variants

Rare missense and truncating variants are carried at similar rates in RARRES1; this gene does not show strong loss-of-function constraint by this measure. 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 210	1 in 1,900
South Asian	~43k	1 in 140	1 in 420
Remaining (unassigned)	~30k	1 in 140	1 in 220
European (Finnish)	~27k	1 in 680	1 in 5,100
Admixed American	~22k	1 in 110	1 in 400
African / African American	~21k	1 in 99	1 in 180
East Asian	~20k	1 in 110	≈ 1 in 20,000
Ashkenazi Jewish	~13k	1 in 1,400	1 in 830
Middle Eastern	~2,884	1 in 280	≈ 1 in 620

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): 4 of 6 coding exons well covered in gnomAD exomes; exons 1, 5 marginal. Genomes: all 6.? see exons ↓