KLHDC8A

kelch domain containing 8A

Basic information

Region (hg38): 1:205336061-205357090

Links

ENSG00000162873 ∙ NCBI:55220 ∙ OMIM:614503 ∙ HGNC:25573 ∙ Uniprot:Q8IYD2 ∙ 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 KLHDC8A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KLHDC8A 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			18			18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	0	0

Variants in KLHDC8A

This is a list of pathogenic ClinVar variants found in the KLHDC8A region.

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

Position	Type	Phenotype	Significance	ClinVar
1-205337431-C-T		not specified	Uncertain significance (Jun 10, 2024)
1-205337461-C-T		not specified	Uncertain significance (Apr 25, 2022)
1-205337479-T-C		not specified	Uncertain significance (Feb 17, 2023)
1-205337551-G-A		not specified	Uncertain significance (Jun 03, 2022)
1-205337553-T-C		not specified	Uncertain significance (May 27, 2022)
1-205338518-C-T		not specified	Uncertain significance (Jan 27, 2022)
1-205338519-G-A		not specified	Uncertain significance (Feb 14, 2024)
1-205338564-G-C		not specified	Uncertain significance (Apr 28, 2022)
1-205339206-C-T		not specified	Uncertain significance (Jun 19, 2024)
1-205339251-G-A		not specified	Uncertain significance (Jul 09, 2021)
1-205339365-C-G		not specified	Uncertain significance (Apr 18, 2023)
1-205339403-C-T		not specified	Uncertain significance (Jul 14, 2021)
1-205339682-G-T		not specified	Uncertain significance (Nov 07, 2022)
1-205339720-C-A		not specified	Uncertain significance (Sep 23, 2023)
1-205339724-A-G		not specified	Uncertain significance (Apr 22, 2022)
1-205339752-G-A		not specified	Uncertain significance (Dec 22, 2023)
1-205339767-G-C		not specified	Uncertain significance (Apr 01, 2024)
1-205343247-T-C		not specified	Uncertain significance (May 29, 2024)
1-205343346-C-T		not specified	Uncertain significance (Jul 25, 2023)
1-205343586-T-C		not specified	Uncertain significance (Aug 02, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KLHDC8A	protein_coding	protein_coding	ENST00000367156	5	20999

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.45e-7	0.568	125703	0	45	125748	0.000179

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.896	200	239	0.837	0.0000154	2249
Missense in Polyphen		49	66.572	0.73605		624
Synonymous	-0.0245	98	97.7	1.00	0.00000619	735
Loss of Function	0.964	12	16.2	0.741	0.00000106	148

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000423	0.000420
Ashkenazi Jewish	0.00	0.00
East Asian	0.000218	0.000217
Finnish	0.00	0.00
European (Non-Finnish)	0.000214	0.000211
Middle Eastern	0.000218	0.000217
South Asian	0.000197	0.000196
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: -1.11
• rvis_percentile_EVS: 6.72

Haploinsufficiency Scores

• pHI: 0.165
• hipred: N
• hipred_score: 0.478
• ghis: 0.479

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.219

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Klhdc8a