ZNF75D

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

Basic information

Region (hg38): X:135248590-135344109

Previous symbols: [ "ZNF82", "ZNF75" ]

Links

ENSG00000186376 ∙ NCBI:7626 ∙ OMIM:314997 ∙ HGNC:13145 ∙ Uniprot:P51815 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ZNF75D gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF75D gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				2	1	3
missense			22	2		24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	4	1

Variants in ZNF75D

This is a list of pathogenic ClinVar variants found in the ZNF75D region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
X-135287157-A-G		not specified	Uncertain significance (Jan 23, 2024)
X-135287175-G-A		not specified	Uncertain significance (Jul 26, 2022)
X-135287188-T-C			Likely benign (Jul 01, 2022)
X-135287201-G-A		not specified	Uncertain significance (Apr 26, 2023)
X-135287320-T-G		not specified	Uncertain significance (Jan 07, 2022)
X-135287327-G-T		not specified	Uncertain significance (Aug 02, 2023)
X-135287348-C-T		not specified	Uncertain significance (Aug 02, 2023)
X-135287378-C-G		not specified	Uncertain significance (Feb 28, 2023)
X-135287570-C-T		Abnormality of neuronal migration	Benign (Oct 31, 2014)
X-135287619-G-A			Uncertain significance (Nov 23, 2022)
X-135287619-G-C		not specified	Uncertain significance (Jan 07, 2022)
X-135287678-C-T		not specified	Uncertain significance (Apr 26, 2023)
X-135287758-T-G		not specified	Uncertain significance (Jun 24, 2022)
X-135287769-C-T		not specified	Likely benign (May 27, 2022)
X-135287783-T-C		not specified	Uncertain significance (Apr 23, 2024)
X-135287820-T-G		not specified	Uncertain significance (Jan 30, 2024)
X-135291061-C-G		not specified	Uncertain significance (Aug 04, 2023)
X-135291105-A-G		not specified	Uncertain significance (Jan 08, 2024)
X-135291484-C-T			Benign (Nov 18, 2017)
X-135292341-C-G		not specified	Uncertain significance (May 23, 2023)
X-135292464-G-A		not specified	Uncertain significance (Dec 13, 2022)
X-135293775-G-A			Likely benign (Nov 01, 2022)
X-135293810-T-C		not specified	Uncertain significance (Jun 07, 2023)
X-135293843-T-C		not specified	Uncertain significance (Aug 12, 2021)
X-135293937-G-C		not specified	Uncertain significance (Nov 07, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF75D	protein_coding	protein_coding	ENST00000370766	5	95146

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000265	0.937	125465	95	167	125727	0.00104

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.381	167	181	0.920	0.0000125	3403
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000220	0.000220
Ashkenazi Jewish	0.0291	0.0214
East Asian	0.0000732	0.0000544
Finnish	0.0000628	0.0000462
European (Non-Finnish)	0.000392	0.000281
Middle Eastern	0.0000732	0.0000544
South Asian	0.0000556	0.0000327
Other	0.00178	0.00130

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in transcriptional regulation.
• Pathway: Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription (Consensus)

Intolerance Scores

• loftool: 0.928
• rvis_EVS: -0.09
• rvis_percentile_EVS: 46.74

Haploinsufficiency Scores

• pHI: 0.102
• hipred: N
• hipred_score: 0.148
• ghis: 0.508

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.00307

Gene Damage Prediction

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

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II
• Cellular component: nucleus
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;zinc ion binding