XKR9

XK related 9, the group of XK related family

Basic information

Region (hg38): 8:70669339-70790371

Links

ENSG00000221947 ∙ NCBI:389668 ∙ ∙ HGNC:20937 ∙ Uniprot:Q5GH70 ∙ 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 XKR9 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the XKR9 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			23	2		25
nonsense					1	1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	23	2	1

Variants in XKR9

This is a list of pathogenic ClinVar variants found in the XKR9 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-70681262-G-C		not specified	Uncertain significance (Mar 07, 2024)
8-70681318-G-A		not specified	Uncertain significance (Jul 20, 2021)
8-70706933-G-T		not specified	Uncertain significance (Sep 16, 2021)
8-70706950-A-G		not specified	Uncertain significance (Aug 17, 2022)
8-70706965-C-A		not specified	Uncertain significance (Jan 31, 2023)
8-70706974-A-C		not specified	Likely benign (Aug 12, 2021)
8-70706999-C-A		not specified	Uncertain significance (Dec 07, 2023)
8-70707011-A-C		not specified	Uncertain significance (Mar 23, 2023)
8-70707018-C-A		not specified	Uncertain significance (Dec 03, 2021)
8-70707091-G-A		not specified	Uncertain significance (Jan 09, 2024)
8-70707118-T-C		not specified	Uncertain significance (Nov 22, 2023)
8-70707139-C-T		not specified	Uncertain significance (Dec 27, 2023)
8-70707148-G-T		not specified	Uncertain significance (Apr 27, 2024)
8-70733801-G-A		not specified	Uncertain significance (Jun 29, 2022)
8-70733837-A-G		not specified	Uncertain significance (May 31, 2023)
8-70733838-C-G		not specified	Uncertain significance (Apr 18, 2024)
8-70733849-C-T			Benign (Mar 29, 2018)
8-70733851-A-C		not specified	Uncertain significance (Jan 30, 2024)
8-70733901-G-A			Likely benign (Feb 01, 2024)
8-70733906-A-C		not specified	Uncertain significance (Sep 20, 2023)
8-70733953-G-A		not specified	Uncertain significance (Mar 07, 2024)
8-70733976-T-A		not specified	Uncertain significance (Mar 21, 2023)
8-70734039-C-T		not specified	Uncertain significance (Jan 05, 2022)
8-70734089-T-C		not specified	Uncertain significance (Jun 22, 2021)
8-70734125-T-G		not specified	Uncertain significance (Jan 03, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
XKR9	protein_coding	protein_coding	ENST00000408926	3	121007

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.06e-9	0.108	124244	40	1423	125707	0.00584

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.71	252	186	1.35	0.00000834	2465
Missense in Polyphen		59	49.239	1.1982		685
Synonymous	-0.775	73	65.0	1.12	0.00000319	682
Loss of Function	0.0433	13	13.2	0.987	5.52e-7	184

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00370	0.00369
Ashkenazi Jewish	0.00	0.00
East Asian	0.0686	0.0671
Finnish	0.0000464	0.0000462
European (Non-Finnish)	0.000715	0.000713
Middle Eastern	0.0686	0.0671
South Asian	0.00195	0.00177
Other	0.00403	0.00376

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.663
• rvis_EVS: 1.24
• rvis_percentile_EVS: 93.39

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.144

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.593

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Xkr9

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