ZMAT1

Chr X

zinc finger matrin-type 1

NCBI Gene: 84460 ENSG00000166432 UniProt: Q5H9K5 OMIM: 301007

This gene encodes a protein containing C2H2-type zinc fingers similar to those in nuclear matrix protein matrin 3. Mutations cause autosomal recessive intellectual disability with seizures, developmental delay, and behavioral abnormalities. The gene shows low constraint to loss-of-function variants, consistent with recessive inheritance patterns.

OMIM ResearchSummary from RefSeq

This gene encodes a protein containing Cys2-His2 (C2H2)-type zinc fingers, which are similar to those found in the nuclear matrix protein matrin 3. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jan 2012]

OMIM ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

0.78

LOEUF

Mechanism· predicted

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

0.78LOEUF

pLI 0.001

Z-score 2.26

OE 0.43 (0.25–0.78)

Tolerant

Typical tolerance to LoF variation

Missense Constraint?

0.44Z-score

OE missense 0.91 (0.81–1.03)

187 obs / 204.9 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.43 (0.25–0.78)

0≤0.351.4

Missense OE?0.91 (0.81–1.03)

0≤0.61.4

Synonymous OE?0.92

0≤1.21.6

LoF obs/exp: 8 / 18.5Missense obs/exp: 187 / 204.9Syn Z: 0.54

Background carrier burden — how many people carry a rare variant somewhere in ZMAT1?

gnomAD v4 · ~732k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 92

595 rare PASS variants

Rare truncating (LoF)

1 in 1,700

52 rare PASS variants

Rare synonymous (reference)

1 in 240

233 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for ZMAT1. 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)	~561k	1 in 130	1 in 1,700
South Asian	~36k	1 in 110	1 in 610
Remaining (unassigned)	~31k	1 in 87	1 in 2,100
European (Finnish)	~27k	1 in 550	none seen
Admixed American	~23k	1 in 110	≈ 1 in 11,000
African / African American	~21k	1 in 120	≈ 1 in 17,000
East Asian	~20k	1 in 120	none seen
Ashkenazi Jewish	~13k	1 in 490	1 in 1,400
Middle Eastern	~2,757	1 in 110	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): 5 of 6 coding exons well covered in gnomAD exomes; exon 1 marginal. Genomes: all 6.? see exons ↓