MSANTD4

Chr 11

Myb/SANT DNA binding domain containing 4 with coiled-coils

Also known as: KIAA1826

NCBI Gene: 84437 ENSG00000170903 UniProt: Q8NCY6

Located in nucleus. [provided by Alliance of Genome Resources, Jul 2025]

Research

Located in nucleus. [provided by Alliance of Genome Resources, Jul 2025]

ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

0.71

LOEUF

Mechanism· predicted

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?

0.71LOEUF

pLI 0.014

Z-score 2.42

OE 0.36 (0.20–0.71)

Tolerant

Typical tolerance to LoF variation

Missense Constraint?

0.86Z-score

OE missense 0.82 (0.72–0.94)

151 obs / 184.0 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.36 (0.20–0.71)

0≤0.351.4

Missense OE?0.82 (0.72–0.94)

0≤0.61.4

Synonymous OE?0.95

0≤1.21.6

LoF obs/exp: 6 / 16.6Missense obs/exp: 151 / 184.0Syn Z: 0.35

Background carrier burden — how many people carry a rare variant somewhere in MSANTD4?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 220

380 rare PASS variants

Rare truncating (LoF)

1 in 6,700

37 rare PASS variants

Rare synonymous (reference)

1 in 300

147 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for MSANTD4. 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 170	1 in 7,900
South Asian	~43k	1 in 250	1 in 7,200
Remaining (unassigned)	~30k	1 in 270	1 in 6,000
European (Finnish)	~27k	1 in 180	none seen
Admixed American	~22k	1 in 260	≈ 1 in 22,000
African / African American	~21k	1 in 310	1 in 1,400
East Asian	~20k	1 in 380	≈ 1 in 6,600
Ashkenazi Jewish	~13k	1 in 840	none seen
Middle Eastern	~2,884	1 in 290	≈ 1 in 2,900

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 2 coding exons well covered in gnomAD exomes and genomes.? see exons ↓