XKR4

XK related 4, the group of XK related family

Basic information

Region (hg38): 8:55102027-55542054

Links

ENSG00000206579 ∙ NCBI:114786 ∙ ∙ HGNC:29394 ∙ Uniprot:Q5GH76 ∙ 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 XKR4 gene.

• Inborn genetic diseases (17 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the XKR4 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					1	1
missense			15	2		17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	2	1

Variants in XKR4

This is a list of pathogenic ClinVar variants found in the XKR4 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-55102655-C-G		not specified	Uncertain significance (Apr 07, 2023)
8-55102717-T-G		not specified	Uncertain significance (Jul 20, 2021)
8-55102802-G-A		not specified	Uncertain significance (Feb 28, 2024)
8-55102876-G-A		not specified	Likely benign (Apr 07, 2023)
8-55102927-C-A		not specified	Uncertain significance (Dec 21, 2022)
8-55102969-G-A		not specified	Uncertain significance (Mar 29, 2022)
8-55103000-T-G		not specified	Uncertain significance (Feb 12, 2024)
8-55103018-C-T		not specified	Uncertain significance (Nov 19, 2022)
8-55103057-C-T		not specified	Uncertain significance (Sep 29, 2022)
8-55103080-G-A		not specified	Likely benign (Dec 19, 2023)
8-55103161-G-A		not specified	Uncertain significance (Apr 07, 2023)
8-55103185-A-G		not specified	Uncertain significance (Jun 01, 2023)
8-55103192-G-C		not specified	Uncertain significance (Nov 18, 2023)
8-55103206-A-G		not specified	Uncertain significance (Apr 07, 2023)
8-55357689-C-T		not specified	Uncertain significance (Oct 02, 2023)
8-55523379-T-C		not specified	Uncertain significance (Jun 02, 2023)
8-55523754-G-A		not specified	Uncertain significance (Apr 25, 2022)
8-55523796-A-G		not specified	Uncertain significance (Aug 10, 2021)
8-55523851-G-A		not specified	Uncertain significance (Feb 14, 2023)
8-55523894-C-G		not specified	Likely benign (Nov 15, 2021)
8-55523951-C-A			Benign (May 25, 2018)
8-55524138-G-A		not specified	Uncertain significance (Dec 01, 2022)
8-55524180-G-A		not specified	Uncertain significance (May 18, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
XKR4	protein_coding	protein_coding	ENST00000327381	3	439665

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.999	0.000881	125743	0	3	125746	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.64	285	374	0.762	0.0000202	4219
Missense in Polyphen		128	167.74	0.76308		1888
Synonymous	0.870	145	159	0.912	0.00000896	1325
Loss of Function	4.43	1	24.8	0.0404	0.00000145	242

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	0.00	0.00
European (Non-Finnish)	0.00000879	0.00000879
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000356	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.110

Intolerance Scores

• loftool: 0.0178
• rvis_EVS: -0.82
• rvis_percentile_EVS: 11.68

Haploinsufficiency Scores

• pHI: 0.178
• hipred: Y
• hipred_score: 0.800
• ghis: 0.481

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.264

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Xkr4

Gene ontology

• Biological process: engulfment of apoptotic cell;phosphatidylserine exposure on apoptotic cell surface;apoptotic process involved in development
• Cellular component: plasma membrane;membrane;integral component of membrane