ZNF638

protein-coding

zinc finger protein 638, the group of RNA binding motif containing

Gene summary

The protein encoded by this gene is a nucleoplasmic protein. It binds cytidine-rich sequences in double-stranded DNA. This protein has three types of domains: MH1, MH2 (repeated three times) and MH3. It is associated with packaging, transferring, or processing transcripts. Multiple alternatively spliced transcript variants have been found for this gene, but the biological validity of some variants has not been determined. [provided by RefSeq, Jul 2008]

Previous symbols:

ZFML

MANE transcript

NM_014497.5

Inheritance

—

ClinVar variants

U:300B:20

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.09

Max pathogenic AF

—

Genomic locus

chr2:71,276,561-71,435,069

External References & Databases

Ensembl (ENSG00000075292)

Transcript & Mutation Effects

hg38 • Region Span ~158.5 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 ZNF638 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 291

not providedTotal: 7

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_014497.5. 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			4 clinvar	1 clinvar	2 clinvar	7
missense			285 clinvar	17 clinvar		302
nonsense			1 clinvar			1
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			9 clinvar			9
Total	0	0	300	18	2	320

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 59 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_014497.5	RefSeq	NP_055312.2	27	MANE Select
ENST00000264447.9	Ensembl	ENSP00000264447.4	27	MANE Select
NM_001014972.3	RefSeq	NP_001014972.1	27	Standard
NM_001252612.2	RefSeq	NP_001239541.1	27	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

RNA splicing

Molecular Function

double-stranded DNA binding
RNA binding
zinc ion binding

Cellular Component

nucleoplasm
cytoplasm
nuclear speck
intracellular membrane-bounded organelle

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000409544
Coding exons: 27
Length: 158509
Individuals with no LoFs: 125733
Homozygous LoFs: 0
Heterozygous LoFs: 15
Defined: 125748
p: 0.0000596

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.575	1060	1.01e+3	1.05	0.0000507	13049
Missense (PolyPhen)		258	298.35	0.86475		3968
Synonymous	-1.21	371	342	1.08	0.0000171	3708
Loss of Function	7.77	8	85.6	0.0934	0.00000466	1178

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00019	0.00018	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000054	0.000054	rare
Finnish	0.000092	0.000092	rare
European (Non-Finnish)	0.000080	0.000079	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Early regulator of adipogenesis that works as a transcription cofactor of CEBPs, controlling the expression of PPARG and probably of other proadipogenic genes, such as SREBF1 (By similarity). Binds to cytidine clusters in double-stranded DNA (PubMed:8647861). May also regulate alternative splicing of target genes during adipogenesis (By similarity). {ECO:0000250|UniProtKB:Q61464, ECO:0000269|PubMed:8647861}.;

Recessive Scores

pRec: 0.0937

Intolerance Scores

LoFtool: 0.439
RVIS EVS: -1.6
RVIS percentile EVS: 3.02

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): K
Indispensability pred.: E
Indispensability score: 0.559

Gene Damage Prediction

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