XKR7

XK related 7, the group of XK related family

Basic information

Region (hg38): 20:31968151-32003387

Previous symbols: [ "C20orf159" ]

Links

ENSG00000260903 ∙ NCBI:343702 ∙ ∙ HGNC:23062 ∙ Uniprot:Q5GH72 ∙ 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 XKR7 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the XKR7 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			29			29
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	29	0	0

Variants in XKR7

This is a list of pathogenic ClinVar variants found in the XKR7 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-31968215-C-G		not specified	Uncertain significance (Jun 10, 2024)
20-31968234-C-A		not specified	Uncertain significance (Nov 08, 2022)
20-31968236-G-T		not specified	Uncertain significance (Feb 16, 2023)
20-31968245-C-T		not specified	Uncertain significance (Nov 17, 2022)
20-31968290-C-T		not specified	Uncertain significance (Apr 23, 2024)
20-31968303-T-G		not specified	Uncertain significance (Jul 09, 2021)
20-31968384-A-G		not specified	Uncertain significance (May 02, 2024)
20-31968537-G-T		not specified	Uncertain significance (Dec 20, 2023)
20-31968549-C-G		not specified	Uncertain significance (Dec 12, 2023)
20-31968579-G-A		not specified	Uncertain significance (Feb 10, 2023)
20-31968608-G-C		not specified	Uncertain significance (Dec 03, 2021)
20-31968641-G-A		not specified	Uncertain significance (Aug 12, 2021)
20-31968650-C-T		not specified	Uncertain significance (Jun 18, 2021)
20-31968660-C-T		not specified	Uncertain significance (Mar 31, 2022)
20-31968663-C-T		not specified	Uncertain significance (Jun 28, 2023)
20-31995108-C-G		not specified	Uncertain significance (Jul 25, 2023)
20-31995111-G-A		not specified	Uncertain significance (Feb 05, 2024)
20-31995114-G-A		not specified	Uncertain significance (Dec 28, 2023)
20-31996577-C-T		not specified	Uncertain significance (Jun 05, 2024)
20-31996592-G-A		not specified	Uncertain significance (Aug 04, 2021)
20-31996612-G-A		not specified	Uncertain significance (Jun 07, 2023)
20-31996697-A-G		not specified	Uncertain significance (Oct 25, 2023)
20-31996714-G-A		not specified	Uncertain significance (Apr 18, 2023)
20-31996839-C-A		not specified	Uncertain significance (Jun 16, 2023)
20-31996948-G-A		not specified	Uncertain significance (Apr 26, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
XKR7	protein_coding	protein_coding	ENST00000562532	3	35386

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.908	0.0917	125738	0	5	125743	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.57	256	337	0.760	0.0000209	3624
Missense in Polyphen		108	157.88	0.68407		1699
Synonymous	1.41	128	150	0.854	0.00000912	1279
Loss of Function	3.31	2	16.5	0.121	7.08e-7	192

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)	0.0000362	0.0000352
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.0278
• rvis_EVS: -0.36
• rvis_percentile_EVS: 28.93

Haploinsufficiency Scores

• pHI: 0.352
• hipred: Y
• hipred_score: 0.755

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.370

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Xkr7

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