XKR3

XK related 3, the group of XK related family

Basic information

Region (hg38): 22:16783412-16825411

Links

ENSG00000172967 ∙ NCBI:150165 ∙ OMIM:611674 ∙ HGNC:28778 ∙ Uniprot:Q5GH77 ∙ 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 XKR3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the XKR3 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			23			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	23	1	0

Variants in XKR3

This is a list of pathogenic ClinVar variants found in the XKR3 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-16783721-G-A			Likely benign (Jan 01, 2023)
22-16783729-C-T		not specified	Uncertain significance (Jun 24, 2022)
22-16783744-C-T		not specified	Uncertain significance (Mar 03, 2022)
22-16783834-C-A		not specified	Uncertain significance (Apr 08, 2022)
22-16784001-T-C		not specified	Uncertain significance (Jun 22, 2021)
22-16784128-G-A		not specified	Uncertain significance (Sep 01, 2021)
22-16784143-T-A		not specified	Uncertain significance (Oct 12, 2022)
22-16784154-T-C		not specified	Uncertain significance (Mar 01, 2024)
22-16784166-G-A		not specified	Uncertain significance (Jan 04, 2022)
22-16784205-A-G		not specified	Uncertain significance (Aug 28, 2023)
22-16784244-G-C		not specified	Uncertain significance (Dec 30, 2023)
22-16784284-C-G		not specified	Uncertain significance (Mar 29, 2023)
22-16784307-G-A		not specified	Uncertain significance (Jan 17, 2023)
22-16784320-T-C		not specified	Uncertain significance (Oct 06, 2022)
22-16784373-T-C		not specified	Uncertain significance (Dec 22, 2023)
22-16784376-G-A		not specified	Uncertain significance (Mar 04, 2024)
22-16799773-C-T		not specified	Uncertain significance (Jun 30, 2023)
22-16799839-C-A		not specified	Uncertain significance (Jan 09, 2024)
22-16799840-C-T		not specified	Uncertain significance (Aug 12, 2021)
22-16799842-A-T		not specified	Uncertain significance (Dec 15, 2023)
22-16807810-G-T		not specified	Uncertain significance (Dec 14, 2021)
22-16807898-C-T		not specified	Uncertain significance (Dec 02, 2022)
22-16808001-G-C		not specified	Uncertain significance (May 23, 2023)
22-16808010-C-G		not specified	Uncertain significance (Dec 11, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
XKR3	protein_coding	protein_coding	ENST00000331428	3	38288

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0787	0.877	124732	0	25	124757	0.000100

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.10	144	186	0.772	0.00000928	3015
Missense in Polyphen		29	46.037	0.62993		722
Synonymous	1.94	48	68.4	0.702	0.00000352	851
Loss of Function	1.71	3	8.33	0.360	4.17e-7	106

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.000334	0.000334
Finnish	0.0000470	0.0000464
European (Non-Finnish)	0.000142	0.000141
Middle Eastern	0.000334	0.000334
South Asian	0.0000761	0.0000654
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.838
• rvis_EVS: 1.21
• rvis_percentile_EVS: 93.09

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.187

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.000443

Gene Damage Prediction

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

Gene ontology

• Cellular component: plasma membrane;integral component of membrane