XKR6

XK related 6, the group of MicroRNA protein coding host genes|XK related family

Basic information

Region (hg38): 8:10896044-11201833

Previous symbols: [ "C8orf7", "C8orf21", "C8orf5" ]

Links

ENSG00000171044 ∙ NCBI:286046 ∙ ∙ HGNC:27806 ∙ Uniprot:Q5GH73 ∙ 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 XKR6 gene.

• Inborn genetic diseases (23 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the XKR6 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	2		24
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	2	0

Variants in XKR6

This is a list of pathogenic ClinVar variants found in the XKR6 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-10897983-T-C		not specified	Uncertain significance (May 22, 2023)
8-10898020-C-T		not specified	Uncertain significance (Jan 09, 2024)
8-10898091-G-C			Uncertain significance (Jul 15, 2022)
8-10898139-G-A		not specified	Uncertain significance (Mar 04, 2024)
8-10898143-G-A		not specified	Uncertain significance (Feb 17, 2024)
8-10898164-T-A		not specified	Uncertain significance (Nov 29, 2023)
8-10898214-G-A		not specified	Uncertain significance (Dec 02, 2021)
8-10898250-G-A		not specified	Uncertain significance (Oct 05, 2021)
8-10898335-C-T		not specified	Uncertain significance (Nov 12, 2021)
8-10898413-C-T		not specified	Uncertain significance (Sep 07, 2022)
8-10898421-G-A		not specified	Uncertain significance (Jan 06, 2023)
8-10898481-G-A		not specified	Uncertain significance (Jan 03, 2022)
8-10898508-G-A		not specified	Uncertain significance (Dec 09, 2023)
8-10898556-C-T		not specified	Uncertain significance (Sep 14, 2023)
8-10898670-T-C		not specified	Uncertain significance (Dec 21, 2022)
8-10898710-C-T		not specified	Uncertain significance (Feb 15, 2023)
8-10898713-A-G		not specified	Uncertain significance (Oct 13, 2023)
8-10898820-C-T		not specified	Uncertain significance (Apr 28, 2023)
8-10898836-C-T		not specified	Uncertain significance (Dec 15, 2022)
8-10898850-C-T		not specified	Uncertain significance (Dec 05, 2022)
8-10898851-G-A		not specified	Uncertain significance (Feb 28, 2024)
8-11200666-G-A		not specified	Uncertain significance (Aug 01, 2022)
8-11200694-C-T		not specified	Uncertain significance (Apr 12, 2022)
8-11200754-C-A		not specified	Uncertain significance (Dec 08, 2023)
8-11200916-C-G		not specified	Uncertain significance (Dec 26, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
XKR6	protein_coding	protein_coding	ENST00000416569	3	305321

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.999	0.000664	125743	0	2	125745	0.00000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.01	262	371	0.706	0.0000211	4090
Missense in Polyphen		80	166.48	0.48055		1749
Synonymous	-2.65	204	161	1.27	0.00000971	1352
Loss of Function	4.50	1	25.5	0.0392	0.00000165	228

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)	0.0000176	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.104

Intolerance Scores

• loftool: 0.106
• rvis_EVS: -0.82
• rvis_percentile_EVS: 11.68

Haploinsufficiency Scores

• pHI: 0.319
• hipred: Y
• hipred_score: 0.728
• ghis: 0.457

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.258

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Xkr6

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