ZNF630

protein-coding

zinc finger protein 630, the group of Zinc fingers C2H2-type

Gene summary

This gene encodes a protein containing an N-terminal Kruppel-associated box-containing (KRAB) domain and 13 Kruppel-type C2H2 zinc finger domains. This gene resides on an area of chromosome X that has been implicated in nonsyndromic X-linked cognitive disability. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2013]

MANE transcript

NM_001282201.2

Inheritance

—

ClinVar variants

U:70B:5

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.61

Max pathogenic AF

—

Genomic locus

chrX:47,983,356-48,071,658

External References & Databases

Ensembl (ENSG00000221994)

Transcript & Mutation Effects

hg38 • Region Span ~88.3 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 ZNF630 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 53

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001282201.2. 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			2 clinvar	2 clinvar		4
missense			60 clinvar	3 clinvar		63
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			8 clinvar			8
Total	0	0	70	5	0	75

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 23 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001282201.2	RefSeq	NP_001269130.1	4	MANE Select
ENST00000276054.9	Ensembl	ENSP00000354683.4	4	MANE Select
NM_001037735.4	RefSeq	NP_001032824.2	4	Standard
NM_001190255.3	RefSeq	NP_001177184.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

regulation of transcription, DNA-templated

Molecular Function

DNA binding
metal ion binding

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000409324
Coding exons: 4
Length: 88270
Individuals with no LoFs: 125214
Homozygous LoFs: 16
Heterozygous LoFs: 40
Defined: 125270
p: 0.000224

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.145	230	224	1.03	0.0000150	4361
Missense (PolyPhen)		51	57.248	0.89087		1173
Synonymous	0.722	69	77.1	0.895	0.00000513	1161
Loss of Function	1.31	8	13.1	0.610	8.21e-7	321

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000077	0.000062	rare
Latino/Admixed American	0.0014	0.00099	notable
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00022	0.00016	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00018	0.00012	rare
South Asian	0.00016	0.000098	rare
Other	0.00022	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May be involved in transcriptional regulation.;

Intolerance Scores

LoFtool: 0.862
RVIS EVS: 1.2
RVIS percentile EVS: 92.95

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.539

Gene Damage Prediction

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