KRTCAP2

keratinocyte associated protein 2, the group of Oligosaccharyltransferase complex subunits

Basic information

Region (hg38): 1:155169408-155173475

Links

ENSG00000163463 ∙ NCBI:200185 ∙ OMIM:619029 ∙ HGNC:28942 ∙ Uniprot:Q8N6L1 ∙ 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 KRTCAP2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KRTCAP2 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			4			4
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			4	1		5
Total	0	0	8	1	0

Variants in KRTCAP2

This is a list of pathogenic ClinVar variants found in the KRTCAP2 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-155169478-G-A		not specified	Uncertain significance (Feb 22, 2023)
1-155169525-T-C		not specified	Uncertain significance (Feb 14, 2023)
1-155169544-C-A		not specified	Uncertain significance (Feb 28, 2024)
1-155172591-C-T		not specified	Uncertain significance (Aug 04, 2023)
1-155172887-C-T		not specified	Uncertain significance (May 06, 2024)
1-155173251-C-T		not specified	Likely benign (Oct 05, 2023)
1-155173254-C-T		not specified	Uncertain significance (Jul 19, 2022)
1-155173259-G-A		not specified	Uncertain significance (Dec 08, 2023)
1-155173290-T-C		not specified	Uncertain significance (Apr 20, 2023)
1-155173296-T-C		not specified	Uncertain significance (Apr 12, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KRTCAP2	protein_coding	protein_coding	ENST00000295682	5	4068

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000352	0.623	125723	0	25	125748	0.0000994

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.421	100	88.8	1.13	0.00000392	1029
Missense in Polyphen		21	30.004	0.69991		380
Synonymous	-0.193	40	38.5	1.04	0.00000168	354
Loss of Function	0.658	6	8.01	0.749	4.26e-7	82

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000329	0.000316
Ashkenazi Jewish	0.000211	0.000198
East Asian	0.00	0.00
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.0000976	0.0000879
Middle Eastern	0.00	0.00
South Asian	0.0000654	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as accessory component of the N-oligosaccharyl transferase (OST) complex which catalyzes the transfer of a high mannose oligosaccharide from a lipid-linked oligosaccharide donor to an asparagine residue within an Asn-X-Ser/Thr consensus motif in nascent polypeptide chains. Required for efficient substrate- specific N-glycosylation probably involving the STT3A-containing OST complex. May be involved in N-glycosylation of APP (amyloid- beta precursor protein). Can modulate gamma-secretase cleavage of APP by enhancing endoprotelysis of PSEN1. {ECO:0000269|PubMed:21768116, ECO:0000269|PubMed:22467853, ECO:0000305}.

Recessive Scores

• pRec: 0.109

Intolerance Scores

• loftool: 0.562
• rvis_EVS: -0.16
• rvis_percentile_EVS: 41.25

Haploinsufficiency Scores

• pHI: 0.290
• hipred: N
• hipred_score: 0.325
• ghis: 0.475

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.385

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Krtcap2

Gene ontology

• Biological process: protein N-linked glycosylation via arginine
• Cellular component: cellular_component;oligosaccharyltransferase complex;integral component of membrane
• Molecular function: molecular_function