KHDC4

KH domain containing 4, pre-mRNA splicing factor, the group of Small nucleolar RNA protein coding host genes

Basic information

Region (hg38): 1:155913045-155934413

Previous symbols: [ "KIAA0907" ]

Links

ENSG00000132680 ∙ NCBI:22889 ∙ OMIM:619370 ∙ HGNC:29145 ∙ Uniprot:Q7Z7F0 ∙ 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 KHDC4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KHDC4 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			25			25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	25	0	1

Variants in KHDC4

This is a list of pathogenic ClinVar variants found in the KHDC4 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-155914158-C-T		not specified	Uncertain significance (Mar 29, 2023)
1-155914174-G-A		not specified	Uncertain significance (Dec 21, 2022)
1-155914287-T-G		not specified	Uncertain significance (Jan 17, 2024)
1-155916670-C-T		not specified	Uncertain significance (Jan 03, 2024)
1-155917639-G-A		not specified	Uncertain significance (Aug 16, 2022)
1-155917668-G-A		not specified	Uncertain significance (Jun 10, 2024)
1-155921406-G-A		not specified	Uncertain significance (Apr 22, 2024)
1-155921446-G-A		not specified	Uncertain significance (Jun 12, 2023)
1-155921515-G-T		not specified	Uncertain significance (Mar 07, 2023)
1-155921538-G-T		not specified	Uncertain significance (Jul 05, 2023)
1-155921567-A-T		not specified	Uncertain significance (Jan 10, 2022)
1-155921568-T-C		not specified	Uncertain significance (Apr 12, 2022)
1-155921617-G-T		not specified	Uncertain significance (Aug 02, 2023)
1-155926722-G-A		not specified	Uncertain significance (Dec 27, 2023)
1-155926725-A-T		not specified	Uncertain significance (Jul 14, 2021)
1-155926731-G-A		not specified	Uncertain significance (Sep 22, 2023)
1-155926749-G-A		not specified	Uncertain significance (Jul 28, 2021)
1-155926806-T-C		not specified	Uncertain significance (Feb 16, 2023)
1-155926816-T-A		not specified	Uncertain significance (Mar 18, 2024)
1-155929363-T-C		not specified	Uncertain significance (May 10, 2024)
1-155929366-G-C		not specified	Uncertain significance (Feb 13, 2024)
1-155929830-G-A		not specified	Uncertain significance (Jul 09, 2021)
1-155933730-G-A		not specified	Uncertain significance (Oct 05, 2023)
1-155933773-T-C		not specified	Uncertain significance (Sep 19, 2022)
1-155933782-C-G		not specified	Uncertain significance (Sep 26, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KHDC4	protein_coding	protein_coding	ENST00000368321	14	21358

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.969	0.0308	125738	0	10	125748	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.74	241	330	0.730	0.0000161	3925
Missense in Polyphen		58	119.57	0.48507		1399
Synonymous	0.733	107	117	0.914	0.00000569	1274
Loss of Function	4.50	5	32.8	0.152	0.00000179	374

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.000282	0.000277
European (Non-Finnish)	0.0000176	0.0000176
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000329	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: RNA-binding protein involved in pre-mRNA splicing (PubMed:19641227). Interacts with the PRP19C/Prp19 complex/NTC/Nineteen complex which is part of the spliceosome (PubMed:19641227). Involved in regulating splice site selection (PubMed:19641227). Binds preferentially RNA with A/C rich sequences and poly-C stretches (PubMed:23144703). {ECO:0000269|PubMed:19641227, ECO:0000269|PubMed:23144703}.

Recessive Scores

• pRec: 0.113

Intolerance Scores

• rvis_EVS: -0.58
• rvis_percentile_EVS: 18.44

Haploinsufficiency Scores

• pHI: 0.440
• hipred: Y
• hipred_score: 0.591
• ghis: 0.651

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Khdc4

Gene ontology

• Biological process: mRNA splice site selection
• Cellular component: nucleus;spliceosomal complex;cytoplasm
• Molecular function: RNA binding;protein binding