ZNF142

Chr 2AR

zinc finger protein 142

Also known as: HA4654, NEDISHM, pHZ-49

NCBI Gene: 7701 ENSG00000115568 UniProt: P52746 OMIM: 604083

The protein is a transcriptional regulator containing 31 C2H2-type zinc fingers from the Kruppel family. Biallelic mutations cause a neurodevelopmental disorder with impaired speech and hyperkinetic movements, inherited in an autosomal recessive pattern. The gene shows relatively low constraint to loss-of-function variants.

OMIM ResearchSummary from RefSeq, OMIM, UniProt

The protein encoded by this gene belongs to the Kruppel family of C2H2-type zinc finger proteins. It contains 31 C2H2-type zinc fingers and may be involved in transcriptional regulation. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jan 2013]

OMIM ResearchGenerating clinical summary…

LOFmechanismARLOEUF 0.791 OMIM phenotype

Clinical Summary— ZNF142

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Population Constraint (gnomAD)

Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.

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ClinVar Variants

46 unique Pathogenic / Likely Pathogenic· 342 VUS of 514 total submissions

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Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

0.79LOEUF

pLI 0.000

Z-score 2.84

OE 0.59 (0.45–0.79)

Tolerant

Typical tolerance to LoF variation

Missense Constraint?

0.24Z-score

OE missense 0.98 (0.93–1.03)

962 obs / 983.3 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.59 (0.45–0.79)

0≤0.351.4

Missense OE?0.98 (0.93–1.03)

0≤0.61.4

Synonymous OE?0.97

0≤1.21.6

LoF obs/exp: 34 / 57.2Missense obs/exp: 962 / 983.3Syn Z: 0.51

ClinVar Variant Classifications

514 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic25

Likely Pathogenic21

VUS342

Likely Benign82

Benign22

Conflicting7

Pathogenic

Likely Pathogenic

342

VUS

Likely Benign

Benign

Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	LoF	Missense + Inframe	Non-coding	Synonymous	Total
Pathogenic	24	0	1	0	25
Likely Pathogenic	18	3	0	0	21
VUS	2	339	1	0	342
Likely Benign	0	38	1	43	82
Benign	0	7	8	7	22
Conflicting	—				7
Total	44	387	11	50	499

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

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27 pathogenic / likely-pathogenic (of 30) ClinVar copy-number / structural variants overlap ZNF142 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →