KLHDC4

kelch domain containing 4

Basic information

Region (hg38): 16:87696485-87765992

Links

ENSG00000104731 ∙ NCBI:54758 ∙ ∙ HGNC:25272 ∙ Uniprot:Q8TBB5 ∙ 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 KLHDC4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KLHDC4 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			59	8		67
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	59	8	0

Variants in KLHDC4

This is a list of pathogenic ClinVar variants found in the KLHDC4 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-87696571-C-G			Benign (Dec 31, 2019)
16-87696581-G-T		Inborn genetic diseases	Uncertain significance (Dec 12, 2022)
16-87696602-T-C		not specified	Uncertain significance (May 16, 2024)
16-87696605-T-C		Inborn genetic diseases	Uncertain significance (Jun 17, 2024)
16-87696611-T-A			Uncertain significance (Jul 01, 2022)
16-87696624-C-T			Likely benign (Mar 06, 2018)
16-87696648-C-A		Inborn genetic diseases	Uncertain significance (Mar 04, 2024)
16-87708392-C-T		not specified	Uncertain significance (Sep 01, 2021)
16-87708398-C-G		not specified	Uncertain significance (Dec 20, 2023)
16-87708404-C-T		not specified	Uncertain significance (Mar 17, 2023)
16-87708409-C-G		not specified	Uncertain significance (May 29, 2024)
16-87708447-C-A		not specified	Uncertain significance (Mar 07, 2024)
16-87709285-G-A		not specified	Likely benign (Dec 06, 2021)
16-87709294-G-T		not specified	Likely benign (Jul 14, 2021)
16-87709345-C-T		not specified	Uncertain significance (Jan 22, 2024)
16-87709346-G-A		not specified	Uncertain significance (Jul 12, 2022)
16-87709348-T-C		not specified	Uncertain significance (Oct 04, 2022)
16-87709375-A-T		not specified	Uncertain significance (Dec 27, 2023)
16-87709406-T-C		not specified	Uncertain significance (Apr 04, 2024)
16-87709418-G-A		not specified	Uncertain significance (May 05, 2023)
16-87709421-G-C		not specified	Uncertain significance (Jul 25, 2023)
16-87709439-G-A		not specified	Uncertain significance (Jun 17, 2024)
16-87709442-T-C		not specified	Likely benign (Oct 25, 2023)
16-87709445-C-T		not specified	Likely benign (Apr 22, 2022)
16-87709448-C-A		not specified	Uncertain significance (May 23, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KLHDC4	protein_coding	protein_coding	ENST00000270583	11	69508

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.56e-31	3.31e-7	125344	0	404	125748	0.00161

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-2.62	468	334	1.40	0.0000210	3358
Missense in Polyphen		154	103.76	1.4842		1088
Synonymous	-4.09	214	150	1.42	0.0000117	996
Loss of Function	-2.23	39	26.6	1.47	0.00000113	329

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00427	0.00426
Ashkenazi Jewish	0.000994	0.000993
East Asian	0.00191	0.00190
Finnish	0.00513	0.00514
European (Non-Finnish)	0.00118	0.00114
Middle Eastern	0.00191	0.00190
South Asian	0.00105	0.00105
Other	0.000819	0.000815

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.102

Intolerance Scores

• loftool: 0.957
• rvis_EVS: 1.08
• rvis_percentile_EVS: 91.76

Haploinsufficiency Scores

• pHI: 0.261
• hipred: N
• hipred_score: 0.352
• ghis: 0.522

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.651

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Klhdc4

Gene ontology

• Molecular function: protein binding