CCDC169-SOHLH2

Chr 13

CCDC169-SOHLH2 readthrough

Also known as: C13orf38-SOHLH2

This gene encodes a fusion protein containing sequences from both C13orf38 and SOHLH2 that arises from natural read-through transcription between these neighboring genes. The gene is highly constrained against loss-of-function variants (pLI = 0.001, LOEUF = 0.61), suggesting it plays an important biological role. No specific disease associations or inheritance patterns have been established for mutations in this fusion gene.

ResearchSummary from RefSeq

This locus represents naturally occurring read-through transcription between the neighboring C13orf38 (chromosome 13 open reading frame 38) and SOHLH2 (spermatogenesis and oogenesis specific basic helix-loop-helix 2) genes. The read-through transcript encodes a fusion protein that shares sequence identity with the products of each individual gene. [provided by RefSeq, Nov 2010]

ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

0.61

LOEUF

—

Mechanism

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?

0.61LOEUF

pLI 0.001

Z-score 3.12

OE 0.36 (0.22–0.61)

Tolerant

Typical tolerance to LoF variation

Missense Constraint?

1.03Z-score

OE missense 0.82 (0.73–0.92)

212 obs / 258.7 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.36 (0.22–0.61)

0≤0.351.4

Missense OE?0.82 (0.73–0.92)

0≤0.61.4

Synonymous OE?0.97

0≤1.21.6

LoF obs/exp: 10 / 27.8Missense obs/exp: 212 / 258.7Syn Z: 0.22

Background carrier burden — how many people carry a rare variant somewhere in CCDC169-SOHLH2?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 110

539 rare PASS variants

Rare truncating (LoF)

1 in 2,100

70 rare PASS variants

Rare synonymous (reference)

1 in 400

224 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for CCDC169-SOHLH2. 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 160	1 in 3,200
South Asian	~43k	1 in 65	1 in 2,500
Remaining (unassigned)	~30k	1 in 91	1 in 1,500
European (Finnish)	~27k	1 in 390	1 in 1,400
Admixed American	~22k	1 in 88	1 in 1,600
African / African American	~21k	1 in 97	≈ 1 in 6,400
East Asian	~20k	1 in 150	≈ 1 in 9,900
Ashkenazi Jewish	~13k	1 in 920	none seen
Middle Eastern	~2,884	1 in 140	none seen

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): All 15 coding exons well covered in gnomAD exomes and genomes.? see exons ↓