ZC2HC1C

protein-coding

zinc finger C2HC-type containing 1C, the group of Zinc fingers C2HC-type

Gene summary

Predicted to enable zinc ion binding activity. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

C14orf140
FAM164C

MANE transcript

NM_024643.4

Inheritance

ClinVar variants

U:63B:10

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.84

Max pathogenic AF

—

Genomic locus

chr14:75,064,109-75,119,502

External References & Databases

Ensembl (ENSG00000119703)

Transcript & Mutation Effects

hg38 • Region Span ~55.4 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

neurodevelopmental disorderLIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0700092

Submitter: Ambry Genetics

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ZC2HC1C variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 70

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_024643.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar			1
missense			62 clinvar	9 clinvar		71
nonsense						0
start loss						0
frameshift				1 clinvar		1
splice donor/acceptor (+/-2bp)						0
Total	0	0	63	10	0	73

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 37 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_024643.4	RefSeq	NP_078919.2	2	MANE Select
ENST00000524913.3	Ensembl	ENSP00000435550.1	2	MANE Select
NM_001042430.3	RefSeq	NP_001035895.1	2	Standard
NM_001330191.2	RefSeq	NP_001317120.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

protein binding
metal ion binding

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000524913
Coding exons: 2
Length: 14254
Individuals with no LoFs: 124239
Homozygous LoFs: 0
Heterozygous LoFs: 4
Defined: 124243
p: 0.0000161

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.0112	249	249	1.00	0.0000141	2994
Missense (PolyPhen)		57	49.619	1.1488		636
Synonymous	0.165	100	102	0.979	0.00000608	891
Loss of Function	0.605	15	17.8	0.845	0.00000110	190

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0.00013	0.00013	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0567

Intolerance Scores

RVIS EVS: 0.4
RVIS percentile EVS: 76.31

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.114

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium