ZNG1C

Zn regulated GTPase metalloprotein activator 1C

Basic information

Region (hg38): 9:68232002-68300035

Previous symbols: [ "CBWD3" ]

Links

ENSG00000196873 ∙ NCBI:445571 ∙ OMIM:611080 ∙ HGNC:18519 ∙ Uniprot:Q5JTY5 ∙ 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 ZNG1C gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNG1C 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						0
missense			8			8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	8	0	0

Variants in ZNG1C

This is a list of pathogenic ClinVar variants found in the ZNG1C region.

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

Position	Type	Phenotype	Significance	ClinVar
9-68247661-A-G		not specified	Uncertain significance (Mar 30, 2024)
9-68247685-A-G		not specified	Uncertain significance (Jul 26, 2022)
9-68256935-A-G		not specified	Uncertain significance (Jan 20, 2023)
9-68297603-A-T		not specified	Uncertain significance (Jul 27, 2021)
9-68298997-G-T		not specified	Uncertain significance (Feb 28, 2023)
9-68299009-G-T		not specified	Uncertain significance (Sep 13, 2023)
9-68299062-C-G		not specified	Uncertain significance (Jan 03, 2024)
9-68299064-C-T		not specified	Uncertain significance (May 31, 2023)
9-68299579-T-A		not specified	Uncertain significance (Dec 26, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNG1C	protein_coding	protein_coding	ENST00000360171	15	58533

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000133	0.122	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.218	41	45.1	0.909	0.00000212	2555
Missense in Polyphen		15	14.947	1.0036		766
Synonymous	-0.978	22	16.9	1.30	8.46e-7	701
Loss of Function	-0.643	8	6.26	1.28	3.14e-7	325

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0981

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.187
• ghis: 0.401

Essentials

• essential_gene_CRISPR: E
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0932

Gene Damage Prediction

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

Gene ontology

• Molecular function: ATP binding