ST7-OT4

Chr 7

ST7 overlapping transcript 4

Also known as: NCRNA00042, ST7OT4

ST7-OT4 encodes a long non-coding RNA involved in gene regulation. Mutations cause autosomal recessive intellectual disability with developmental delay and behavioral abnormalities. This gene shows low constraint to loss-of-function variation, consistent with a recessive inheritance pattern where heterozygous carriers are typically unaffected.

Research

ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

1.47

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?

1.47LOEUF

pLI 0.021

Z-score 0.87

OE 0.58 (0.26–1.47)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

0.84Z-score

OE missense 0.73 (0.59–0.91)

58 obs / 79.0 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.58 (0.26–1.47)

0≤0.351.4

Missense OE?0.73 (0.59–0.91)

0≤0.61.4

Synonymous OE?0.64

0≤1.21.6

LoF obs/exp: 3 / 5.1Missense obs/exp: 58 / 79.0Syn Z: 1.52

Background carrier burden — how many people carry a rare variant somewhere in ST7-OT4?

gnomAD v4 · ~160k individuals · PASS only

Rare means allele frequency under

Rare missense

none observed

0 rare PASS variants

Rare truncating (LoF)

1 in 7,000

8 rare PASS variants

Rare synonymous (reference)

none observed

0 rare PASS variants

Rare missense and truncating variants are carried at similar rates in ST7-OT4; 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 · 6 gnomAD groups · rare = under 0.1% in that group

Group	People	Missense	Truncating
European (non-Finnish)	~80k	none seen	1 in 8,700
South Asian	~30k	none seen	1 in 5,900
African / African American	~21k	none seen	≈ 1 in 20,000
Admixed American	~14k	none seen	≈ 1 in 7,300
European (Finnish)	~14k	none seen	≈ 1 in 3,600
East Asian	~4,604	none seen	≈ 1 in 4,600

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.