ZNF75D

protein-coding

zinc finger protein 75D, the group of Zinc fingers C2H2-type|SCAN domain containing

Gene summary

This gene encodes a protein that likely functions as a transcription factor. The protein, which belongs to the ZNF75 family, includes an N-terminal SCAN domain, a KRAB box, and five C2H2-type zinc finger motifs. Another functional gene belonging to this family is located on chromosome 16, while pseudogenes have been identified on chromosomes 11 and 12. Alternative splicing results in multiple transcripts variants. [provided by RefSeq, Jun 2010]

Previous symbols:

ZNF82
ZNF75

MANE transcript

NM_007131.5

Inheritance

—

ClinVar variants

U:97B:15

Top phenotype

Abnormality of neuronal migration

gnomAD constraint

pLI —, LoF o/e 0.53

Max pathogenic AF

—

Genomic locus

chrX:135,248,590-135,344,109

External References & Databases

Ensembl (ENSG00000186376)

Transcript & Mutation Effects

hg38 • Region Span ~95.5 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 ZNF75D variants in ClinVar

4 Conditions Cataloged

not specifiedTotal: 47

not providedTotal: 9

Abnormality of neuronal migrationTotal: 1

Inborn genetic diseasesTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_007131.5. 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			5 clinvar	7 clinvar	1 clinvar	13
missense			79 clinvar	6 clinvar	1 clinvar	86
nonsense			7 clinvar			7
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			6 clinvar			6
Total	0	0	97	13	2	112

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 35 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_007131.5	RefSeq	NP_009062.2	5	MANE Select
ENST00000370766.8	Ensembl	ENSP00000359802.3	5	MANE Select
NM_001185063.2	RefSeq	NP_001171992.1	3	Standard
ENST00000370764.1	Ensembl	ENSP00000359800.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Gene expression (Transcription)
Generic Transcription Pathway
RNA Polymerase II Transcription

Biological Process

regulation of transcription by RNA polymerase II

Molecular Function

DNA-binding transcription factor activity, RNA polymerase II-specific
DNA binding
zinc ion binding

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000370766
Coding exons: 5
Length: 95146
Individuals with no LoFs: 125465
Homozygous LoFs: 95
Heterozygous LoFs: 167
Defined: 125727
p: 0.00104

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.381	167	181	0.920	0.0000125	3403
Missense (PolyPhen)		53	61.773	0.85797		1232
Synonymous	1.07	55	66.0	0.833	0.00000478	897
Loss of Function	1.67	8	15.0	0.534	0.00000100	275

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.00022	0.00017	rare
Ashkenazi Jewish	0.029	0.021	notable
East Asian	0.000073	0.000054	rare
Finnish	0.000063	0.000046	rare
European (Non-Finnish)	0.00039	0.00028	rare
South Asian	0.000056	0.000033	rare
Other	0.0018	0.0013	notable

dbNSFP Gene Annotations

Source: dbNSFP

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

Intolerance Scores

LoFtool: 0.928
RVIS EVS: -0.09
RVIS percentile EVS: 46.74

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.00307

Gene Damage Prediction

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