XKRX

XK related X-linked, the group of XK related family

Basic information

Region (hg38): X:100913445-100929433

Links

ENSG00000182489 ∙ NCBI:402415 ∙ OMIM:300684 ∙ HGNC:29845 ∙ Uniprot:Q6PP77 ∙ 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 XKRX gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the XKRX 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				3		3
missense			16	1		17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	16	4	0

Variants in XKRX

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

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

Position	Type	Phenotype	Significance	ClinVar
X-100914343-C-T		not specified	Uncertain significance (Dec 07, 2021)
X-100914397-T-A		not specified	Uncertain significance (Nov 13, 2023)
X-100914399-C-T		not specified	Likely benign (Jun 19, 2024)
X-100914451-T-C		not specified	Likely benign (Dec 13, 2022)
X-100914532-G-T		not specified	Uncertain significance (Apr 16, 2024)
X-100914581-G-A			Likely benign (Nov 01, 2023)
X-100914582-A-T		not specified	Uncertain significance (Dec 19, 2022)
X-100914594-A-G		not specified	Uncertain significance (Mar 31, 2022)
X-100914600-A-G		not specified	Uncertain significance (Oct 27, 2021)
X-100914653-G-T		not specified	Uncertain significance (Sep 16, 2021)
X-100914674-A-C		not specified	Uncertain significance (Jan 23, 2024)
X-100914769-C-T		not specified	Uncertain significance (Mar 31, 2024)
X-100914780-A-C		not specified	Uncertain significance (Nov 09, 2023)
X-100914814-C-T		not specified	Uncertain significance (Aug 21, 2024)
X-100914840-T-C		not specified	Uncertain significance (Oct 06, 2024)
X-100914867-A-G		not specified	Uncertain significance (Jan 10, 2023)
X-100914880-C-T		not specified	Uncertain significance (Oct 08, 2024)
X-100914888-A-G		not specified	Uncertain significance (Aug 19, 2024)
X-100914916-G-C		not specified	Uncertain significance (Jan 30, 2024)
X-100914923-G-C			Likely benign (Dec 01, 2022)
X-100915072-C-T		not specified	Uncertain significance (Nov 21, 2024)
X-100922922-G-A		not specified	Uncertain significance (Mar 06, 2023)
X-100922963-C-T		not specified	Uncertain significance (Apr 25, 2022)
X-100928017-T-C			Likely benign (Aug 01, 2022)
X-100928134-G-C		not specified	Uncertain significance (Jan 09, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
XKRX	protein_coding	protein_coding	ENST00000372956	3	15992

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000313	0.823	125733	8	4	125745	0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.482	152	170	0.896	0.0000130	2931
Missense in Polyphen		58	73.253	0.79178		1281
Synonymous	0.631	59	65.5	0.901	0.00000464	904
Loss of Function	1.20	7	11.4	0.616	9.24e-7	193

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000365	0.0000365
Ashkenazi Jewish	0.00	0.00
East Asian	0.000296	0.000217
Finnish	0.00	0.00
European (Non-Finnish)	0.0000244	0.0000176
Middle Eastern	0.000296	0.000217
South Asian	0.000262	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.100

Intolerance Scores

• loftool: 0.561
• rvis_EVS: 0.33
• rvis_percentile_EVS: 73.27

Haploinsufficiency Scores

• pHI: 0.221
• hipred: N
• hipred_score: 0.195
• ghis: 0.471

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.307

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Xkrx
• Phenotype: immune system phenotype; hematopoietic system phenotype

Gene ontology

• Cellular component: plasma membrane;integral component of membrane