XKR8

XK related 8, the group of XK related family

Basic information

Region (hg38): 1:27959588-27968093

Links

ENSG00000158156 ∙ NCBI:55113 ∙ OMIM:619940 ∙ HGNC:25508 ∙ Uniprot:Q9H6D3 ∙ 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 XKR8 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the XKR8 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			22	1		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	22	1	0

Variants in XKR8

This is a list of pathogenic ClinVar variants found in the XKR8 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-27960133-G-T		not specified	Uncertain significance (May 30, 2024)
1-27960155-C-T		XKR8-related condition	Likely benign (Aug 26, 2024)
1-27960241-G-T		not specified	Uncertain significance (Jul 12, 2023)
1-27960245-C-G		not specified	Uncertain significance (Mar 24, 2023)
1-27960260-G-C		not specified	Uncertain significance (May 15, 2024)
1-27960311-C-T		not specified	Uncertain significance (May 30, 2024)
1-27960313-C-T		not specified • XKR8-related condition	Uncertain significance (Mar 21, 2024)
1-27960336-T-G		not specified	Uncertain significance (May 30, 2023)
1-27963573-G-A		not specified	Uncertain significance (May 01, 2022)
1-27963628-C-T		not specified	Uncertain significance (May 11, 2022)
1-27963655-C-G		not specified	Uncertain significance (Jan 19, 2022)
1-27963675-C-T		not specified	Uncertain significance (Jan 31, 2023)
1-27966550-G-A		not specified	Uncertain significance (Jun 03, 2022)
1-27966556-C-T		not specified	Uncertain significance (Jun 06, 2023)
1-27966559-C-T		not specified	Uncertain significance (May 13, 2024)
1-27966560-G-A		not specified	Uncertain significance (Jul 25, 2023)
1-27966596-T-C		not specified	Uncertain significance (Sep 22, 2023)
1-27966605-G-A		not specified	Uncertain significance (Jun 16, 2024)
1-27966613-G-A		not specified	Uncertain significance (Dec 26, 2023)
1-27966667-G-A		not specified	Uncertain significance (May 17, 2023)
1-27966695-A-C		not specified	Uncertain significance (Oct 05, 2023)
1-27966775-C-T		not specified	Uncertain significance (May 23, 2023)
1-27966784-G-A		not specified	Uncertain significance (Dec 22, 2023)
1-27966862-C-T		not specified	Uncertain significance (Dec 21, 2022)
1-27966985-G-A		not specified	Uncertain significance (Sep 01, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
XKR8	protein_coding	protein_coding	ENST00000373884	3	8635

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.07e-8	0.207	125681	0	67	125748	0.000266

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.46	154	214	0.719	0.0000131	2455
Missense in Polyphen		43	61.701	0.69691		821
Synonymous	0.493	100	106	0.939	0.00000645	915
Loss of Function	0.300	12	13.2	0.911	7.57e-7	118

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000922	0.000915
Ashkenazi Jewish	0.00	0.00
East Asian	0.00114	0.00114
Finnish	0.0000933	0.0000924
European (Non-Finnish)	0.0000971	0.0000967
Middle Eastern	0.00114	0.00114
South Asian	0.000206	0.000196
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Promotes phosphatidylserine exposure on apoptotic cell surface, possibly by mediating phospholipid scrambling. Phosphatidylserine is a specific marker only present at the surface of apoptotic cells and acts as a specific signal for engulfment. Has no effect on calcium-induced exposure of phosphatidylserine. Activated upon caspase cleavage, suggesting that it does not act prior the onset of apoptosis. {ECO:0000269|PubMed:23845944}.

Recessive Scores

• pRec: 0.0834

Intolerance Scores

• rvis_EVS: -0.6
• rvis_percentile_EVS: 17.75

Haploinsufficiency Scores

• pHI: 0.156
• hipred: N
• hipred_score: 0.153
• ghis: 0.542

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.661

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Xkr8

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