KRTCAP3

keratinocyte associated protein 3

Basic information

Region (hg38): 2:27442365-27446481

Links

ENSG00000157992 ∙ NCBI:200634 ∙ OMIM:619261 ∙ HGNC:28943 ∙ Uniprot:Q53RY4 ∙ 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 KRTCAP3 gene.

• Inborn genetic diseases (15 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KRTCAP3 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			13	2		15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1		1
Total	0	0	13	3	0

Variants in KRTCAP3

This is a list of pathogenic ClinVar variants found in the KRTCAP3 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-27442591-G-T		not specified	Uncertain significance (Feb 03, 2022)
2-27442611-G-A		not specified	Uncertain significance (Feb 21, 2024)
2-27442612-T-C		not specified	Uncertain significance (Aug 16, 2021)
2-27442659-G-T		not specified	Uncertain significance (Sep 12, 2023)
2-27442674-A-G		not specified	Uncertain significance (Oct 17, 2023)
2-27442753-C-T		not specified	Uncertain significance (Dec 18, 2023)
2-27442758-C-G		not specified	Uncertain significance (Feb 08, 2023)
2-27442890-C-A		not specified	Uncertain significance (Oct 12, 2022)
2-27443089-G-A		not specified	Uncertain significance (Dec 07, 2022)
2-27443106-C-A		not specified	Uncertain significance (Jan 05, 2022)
2-27443137-C-T		not specified	Uncertain significance (Aug 30, 2021)
2-27443150-T-G		not specified	Uncertain significance (Jan 09, 2024)
2-27443171-G-A		not specified	Uncertain significance (Oct 04, 2022)
2-27443237-G-A		not specified	Uncertain significance (Sep 20, 2023)
2-27443479-G-A		not specified	Uncertain significance (Jan 23, 2023)
2-27443510-G-A		not specified	Uncertain significance (Jul 06, 2022)
2-27443517-C-A		not specified	Likely benign (Jul 25, 2023)
2-27443528-G-A		not specified	Likely benign (Jun 16, 2023)
2-27444003-C-G		not specified	Uncertain significance (Mar 14, 2023)
2-27444034-C-T		not specified	Uncertain significance (May 10, 2022)
2-27444241-G-A			Likely benign (Oct 31, 2018)
2-27444317-G-A			Benign (Jun 16, 2018)
2-27444430-A-G		not specified • Retinal dystrophy	Benign (Oct 01, 2023)
2-27444437-G-C		Short-rib thoracic dysplasia 10 with or without polydactyly;Retinitis pigmentosa 71	Uncertain significance (Mar 25, 2021)
2-27444446-A-G		Retinal dystrophy	Uncertain significance (Oct 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KRTCAP3	protein_coding	protein_coding	ENST00000543753	6	4116

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000208	0.493	125517	2	229	125748	0.000919

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.229	147	139	1.05	0.00000820	1472
Missense in Polyphen		60	61.039	0.98297		660
Synonymous	-0.497	67	62.0	1.08	0.00000377	561
Loss of Function	0.556	8	9.89	0.809	4.21e-7	117

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00124	0.00123
Ashkenazi Jewish	0.00	0.00
East Asian	0.00133	0.00131
Finnish	0.00	0.00
European (Non-Finnish)	0.00131	0.00127
Middle Eastern	0.00133	0.00131
South Asian	0.000918	0.000915
Other	0.000832	0.000815

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.910
• rvis_EVS: 0.15
• rvis_percentile_EVS: 64.32

Haploinsufficiency Scores

• pHI: 0.215
• hipred: N
• hipred_score: 0.198
• ghis: 0.412

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.259

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Krtcap3

Gene ontology

• Cellular component: integral component of membrane