KLHDC7B

kelch domain containing 7B

Basic information

Region (hg38): 22:50545898-50551023

Links

ENSG00000130487 ∙ NCBI:113730 ∙ ∙ HGNC:25145 ∙ Uniprot:Q96G42 ∙ 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 KLHDC7B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KLHDC7B 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				3		3
missense			38	3		41
nonsense						0
start loss						0
frameshift						0
inframe indel				1		1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	38	7	0

Variants in KLHDC7B

This is a list of pathogenic ClinVar variants found in the KLHDC7B region.

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

Position	Type	Phenotype	Significance	ClinVar
22-50547870-C-CCATCCCCAGCCCTAACCCCAGTCCCAACCCCAGCCCTAAGCCCAGCTCCAACTCCAGCCCCAACCCCAGCCG			Likely benign (Jan 01, 2023)
22-50548022-T-A			Likely benign (Jan 01, 2024)
22-50548034-C-A			Likely benign (Jan 01, 2024)
22-50548188-T-C		not specified	Uncertain significance (Jun 24, 2022)
22-50548221-C-T		not specified	Uncertain significance (Apr 08, 2024)
22-50548228-C-T		not specified	Uncertain significance (Dec 19, 2022)
22-50548312-T-C		not specified	Likely benign (Dec 13, 2021)
22-50548313-A-G		not specified	Likely benign (Aug 10, 2021)
22-50548374-A-T		not specified	Uncertain significance (Jun 16, 2023)
22-50548456-A-C		not specified	Uncertain significance (Dec 19, 2023)
22-50548464-A-T		not specified	Uncertain significance (Jun 18, 2021)
22-50548564-G-T		not specified	Uncertain significance (Nov 14, 2023)
22-50548653-G-A		not specified	Uncertain significance (Jan 24, 2024)
22-50548657-G-A		not specified	Uncertain significance (Sep 19, 2022)
22-50548665-G-A		not specified	Uncertain significance (Dec 15, 2023)
22-50548690-A-C		not specified	Uncertain significance (Nov 01, 2022)
22-50548709-G-C		not specified	Uncertain significance (Jan 03, 2022)
22-50548710-C-T		not specified	Uncertain significance (Oct 05, 2023)
22-50548738-G-A		not specified	Uncertain significance (May 05, 2023)
22-50548743-G-A		not specified	Uncertain significance (Jun 16, 2023)
22-50548747-T-G		not specified	Uncertain significance (Oct 12, 2022)
22-50548749-G-A		not specified	Uncertain significance (Aug 23, 2021)
22-50548750-T-G		not specified	Uncertain significance (Jan 27, 2022)
22-50548756-G-A		not specified	Uncertain significance (Jan 24, 2024)
22-50548762-G-A		not specified	Uncertain significance (Apr 22, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KLHDC7B	protein_coding	protein_coding	ENST00000395676	1	2990

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.19e-9	0.101	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.19	307	371	0.827	0.0000244	3662
Missense in Polyphen		94	120.9	0.77752		1152
Synonymous	0.779	166	179	0.926	0.0000129	1382
Loss of Function	0.115	14	14.5	0.967	8.32e-7	133

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

Haploinsufficiency Scores

• pHI: 0.0810
• hipred: N
• hipred_score: 0.238
• ghis: 0.432

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.281

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Klhdc7b