GHDC

GH3 domain containing

Basic information

Region (hg38): 17:42188799-42194513

Links

ENSG00000167925 ∙ NCBI:84514 ∙ OMIM:608587 ∙ HGNC:24438 ∙ Uniprot:Q8N2G8 ∙ 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 GHDC gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GHDC 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			48	4		52
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	48	4	0

Variants in GHDC

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

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

Position	Type	Phenotype	Significance	ClinVar
17-42189749-C-G		not specified	Uncertain significance (Jan 31, 2022)
17-42189764-A-G		not specified	Uncertain significance (Jul 12, 2023)
17-42189767-G-C		not specified	Uncertain significance (Aug 22, 2023)
17-42189767-G-T		not specified	Likely benign (Jul 09, 2021)
17-42189771-G-A		not specified	Uncertain significance (Jan 31, 2023)
17-42189771-G-C		not specified	Uncertain significance (May 22, 2023)
17-42189818-C-T		not specified	Uncertain significance (Oct 21, 2024)
17-42189872-A-G		not specified	Uncertain significance (Dec 27, 2023)
17-42190227-C-T		not specified	Likely benign (Dec 16, 2024)
17-42190228-G-A		not specified	Uncertain significance (May 10, 2023)
17-42190246-T-C		not specified	Uncertain significance (Nov 14, 2024)
17-42190626-A-G		not specified	Uncertain significance (Sep 23, 2023)
17-42190671-G-T		not specified	Uncertain significance (Dec 21, 2023)
17-42190677-T-C		not specified	Uncertain significance (Nov 08, 2024)
17-42190689-C-T		not specified	Likely benign (May 23, 2023)
17-42190690-G-A		not specified	Uncertain significance (Oct 12, 2021)
17-42190720-C-T		not specified	Uncertain significance (Jun 16, 2024)
17-42190734-C-T		not specified	Uncertain significance (Oct 09, 2024)
17-42190848-C-T		not specified	Uncertain significance (Apr 06, 2022)
17-42190896-G-C		not specified	Uncertain significance (May 23, 2024)
17-42190898-C-A		not specified	Uncertain significance (Jun 05, 2024)
17-42190898-C-T		not specified	Uncertain significance (Dec 01, 2022)
17-42191033-C-T		not specified	Likely benign (May 09, 2023)
17-42191069-T-G		not specified	Uncertain significance (Aug 05, 2024)
17-42191115-C-T		not specified	Uncertain significance (Apr 26, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GHDC	protein_coding	protein_coding	ENST00000301671	8	5715

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.44e-9	0.817	125644	0	104	125748	0.000414

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.884	251	294	0.855	0.0000175	3254
Missense in Polyphen		83	102.57	0.80924		1215
Synonymous	0.760	120	131	0.916	0.00000723	1223
Loss of Function	1.58	17	25.6	0.663	0.00000158	228

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00216	0.00214
Ashkenazi Jewish	0.00	0.00
East Asian	0.000544	0.000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000421	0.000396
Middle Eastern	0.000544	0.000544
South Asian	0.000248	0.000229
Other	0.000185	0.000163

dbNSFP

Source: dbNSFP

• Pathway: Neutrophil degranulation;Innate Immune System;Immune System (Consensus)

Recessive Scores

• pRec: 0.102

Intolerance Scores

• loftool: 0.0798
• rvis_EVS: 0.2
• rvis_percentile_EVS: 67.3

Haploinsufficiency Scores

• pHI: 0.0598
• hipred: N
• hipred_score: 0.145
• ghis: 0.535

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0750

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ghdc

Gene ontology

• Biological process: biological_process;neutrophil degranulation
• Cellular component: extracellular region;nuclear envelope;endoplasmic reticulum;membrane;secretory granule lumen;specific granule lumen
• Molecular function: molecular_function