ZC3H12B

protein-coding

zinc finger CCCH-type containing 12B, the group of Zinc fingers CCCH-type

Gene summary

The protein encoded by this gene belongs to a family of CCCH-type zinc finger proteins that are involved in the proinflammatory activation of macrophages. The exact function of this family member is unknown, but it is thought to function as a ribonuclease. [provided by RefSeq, May 2010]

Previous symbols:

CXorf32

MANE transcript

NM_001010888.4

Inheritance

ClinVar variants

U:95B:10

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.04

Max pathogenic AF

—

Genomic locus

chrX:65,034,788-65,507,887

External References & Databases

Ensembl (ENSG00000102053)

Transcript & Mutation Effects

hg38 • Region Span ~473.1 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

autism spectrum disorderLIMITED

Inheritance Pattern: AD

Disease ID:MONDO:0005258

Submitter: Ambry Genetics

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ZC3H12B variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 57

not providedTotal: 8

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001010888.4. 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			6 clinvar	2 clinvar	1 clinvar	9
missense			79 clinvar	6 clinvar	1 clinvar	86
nonsense			3 clinvar			3
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			7 clinvar			7
Total	0	0	95	8	2	105

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 26 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001010888.4	RefSeq	NP_001010888.3	5	MANE Select
ENST00000338957.5	Ensembl	ENSP00000340839.4	5	MANE Select
ENST00000696368.1	Ensembl	ENSP00000512583.1	5	Standard
ENST00000696368.2	Ensembl	ENSP00000512583.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

nucleic acid phosphodiester bond hydrolysis

Molecular Function

endonuclease activity
metal ion binding

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000338957
Coding exons: 5
Length: 19153
Individuals with no LoFs: 124558
Homozygous LoFs: 2
Heterozygous LoFs: 4
Defined: 124564
p: 0.0000241

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.54	204	335	0.609	0.0000263	5548
Missense (PolyPhen)		49	128.39	0.38166		2085
Synonymous	0.953	105	118	0.889	0.00000854	1614
Loss of Function	4.26	1	23.1	0.0433	0.00000208	362

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000083	0.000065	rare
Latino/Admixed American	0.000074	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000075	0.000056	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000025	0.000018	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May function as RNase and regulate the levels of target RNA species. {ECO:0000305}.;

Recessive Scores

pRec: 0.0965

Intolerance Scores

LoFtool: 0.252
RVIS EVS: -0.47
RVIS percentile EVS: 23.04

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