KHDC1

KH domain containing 1

Basic information

Region (hg38): 6:73241313-73310365

Previous symbols: [ "C6orf148", "C6orf147" ]

Links

ENSG00000135314 ∙ NCBI:80759 ∙ OMIM:611688 ∙ HGNC:21366 ∙ Uniprot:Q4VXA5 ∙ 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 KHDC1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KHDC1 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			21	2		23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	21	2	0

Variants in KHDC1

This is a list of pathogenic ClinVar variants found in the KHDC1 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-73241542-G-A		not specified	Uncertain significance (May 27, 2022)
6-73241560-G-A		not specified	Uncertain significance (Mar 27, 2023)
6-73241569-A-G		not specified	Uncertain significance (Dec 01, 2022)
6-73241582-G-A		not specified	Uncertain significance (Jun 23, 2021)
6-73241597-C-T		not specified	Uncertain significance (Nov 10, 2022)
6-73241609-C-T		not specified	Uncertain significance (Mar 23, 2023)
6-73241647-G-A		not specified	Uncertain significance (Jan 03, 2024)
6-73241660-C-G		not specified	Uncertain significance (Aug 11, 2022)
6-73241684-C-T		not specified	Uncertain significance (Sep 27, 2021)
6-73241710-C-T		not specified	Uncertain significance (Jul 25, 2023)
6-73241711-G-A		not specified	Uncertain significance (Nov 10, 2022)
6-73242057-C-T		not specified	Likely benign (Jun 23, 2021)
6-73242145-C-T		not specified	Uncertain significance (Jan 03, 2024)
6-73242148-G-A		not specified	Uncertain significance (Jan 06, 2023)
6-73242170-C-A		not specified	Uncertain significance (Nov 15, 2021)
6-73242195-T-C		not specified	Uncertain significance (Mar 14, 2023)
6-73242217-G-A		not specified	Uncertain significance (Mar 28, 2023)
6-73242434-C-T		not specified	Uncertain significance (Apr 06, 2024)
6-73242463-T-G		not specified	Uncertain significance (Nov 08, 2021)
6-73242466-G-C		not specified	Likely benign (Nov 05, 2021)
6-73242480-C-G		not specified	Uncertain significance (Dec 06, 2023)
6-73242483-G-A		not specified	Uncertain significance (Aug 17, 2022)
6-73242486-T-C		not specified	Uncertain significance (Mar 01, 2024)
6-73242510-A-G		not specified	Uncertain significance (Nov 30, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KHDC1	protein_coding	protein_coding	ENST00000370384	5	69052

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.13e-10	0.0365	124782	0	19	124801	0.0000761

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.144	129	134	0.965	0.00000737	1534
Missense in Polyphen		35	36.883	0.94896		393
Synonymous	0.244	49	51.2	0.957	0.00000312	467
Loss of Function	-0.556	13	11.0	1.18	5.63e-7	108

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000936	0.0000935
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000116	0.000115
Middle Eastern	0.00	0.00
South Asian	0.000131	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.509
• rvis_EVS: 0.04
• rvis_percentile_EVS: 56.92

Haploinsufficiency Scores

• pHI: 0.0943
• hipred: N
• hipred_score: 0.112
• ghis: 0.562

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0860

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Khdc1c

Gene ontology

• Cellular component: integral component of membrane
• Molecular function: RNA binding