ZC2HC1A

protein-coding

zinc finger C2HC-type containing 1A, 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:

C8orf70
FAM164A

MANE transcript

NM_016010.3

Inheritance

—

ClinVar variants

U:48B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.23

Max pathogenic AF

—

Genomic locus

chr8:78,666,050-78,719,765

External References & Databases

Ensembl (ENSG00000104427)

Transcript & Mutation Effects

hg38 • Region Span ~53.7 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ZC2HC1A variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 44

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_016010.3. 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 clinvar		2
missense			44 clinvar	3 clinvar		47
nonsense			1 clinvar			1
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	48	4	0	52

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 22 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_016010.3	RefSeq	NP_057094.2	9	MANE Select
ENST00000263849.9	Ensembl	ENSP00000263849.3	9	MANE Select
NM_001362969.2	RefSeq	NP_001349898.1	10	Standard
ENST00000519307.2	Ensembl	ENSP00000427797.2	10	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: ENST00000263849
Coding exons: 9
Length: 53719
Individuals with no LoFs: 125715
Homozygous LoFs: 0
Heterozygous LoFs: 15
Defined: 125730
p: 0.0000597

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.409	151	166	0.911	0.00000801	2064
Missense (PolyPhen)		40	62.08	0.64433		809
Synonymous	-0.569	62	56.6	1.10	0.00000274	636
Loss of Function	2.93	4	17.0	0.235	9.00e-7	230

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.000062	rare
Latino/Admixed American	0.000090	0.000087	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000057	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000090	0.000088	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.104

Intolerance Scores

RVIS EVS: 0.02
RVIS percentile EVS: 55.45

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