KRT10-AS1

KRT10 antisense RNA 1, the group of Antisense RNAs

Basic information

Region (hg38): 17:40819071-40836273

Previous symbols: [ "TMEM99" ]

Links

ENSG00000167920 ∙ NCBI:147184 ∙ ∙ HGNC:28305 ∙ Uniprot:Q8N816 ∙ 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 KRT10-AS1 gene.

• not provided (70 variants)
• Bullous ichthyosiform erythroderma (16 variants)
• Inborn genetic diseases (9 variants)
• Congenital reticular ichthyosiform erythroderma (7 variants)
• Annular epidermolytic ichthyosis (2 variants)
• KRT10-related condition (2 variants)
• Bullous ichthyosiform erythroderma;Annular epidermolytic ichthyosis;Congenital reticular ichthyosiform erythroderma (1 variants)
• Epidermolytic acanthoma (1 variants)
• Epidermolytic nevus (1 variants)
• Congenital reticular ichthyosiform erythroderma;Bullous ichthyosiform erythroderma;Annular epidermolytic ichthyosis (1 variants)
• Annular epidermolytic ichthyosis;Congenital reticular ichthyosiform erythroderma;Bullous ichthyosiform erythroderma (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KRT10-AS1 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						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding	26	5	16	11	20	78
Total	26	5	16	11	20

Variants in KRT10-AS1

This is a list of pathogenic ClinVar variants found in the KRT10-AS1 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-40819075-T-C			Uncertain significance (Oct 13, 2023)
17-40819075-TG-GA			Uncertain significance (Dec 02, 2023)
17-40819075-TGG-GAGCTT			Likely benign (Mar 13, 2018)
17-40819075-TGGCCGCCGCCGG-T		KRT10-related disorder	Likely benign (Feb 01, 2024)
17-40819076-G-A		Annular epidermolytic ichthyosis • Congenital reticular ichthyosiform erythroderma • Epidermolytic ichthyosis	Benign (Jan 29, 2024)
17-40819076-GGCCGCCGCCGGAGCTT-AG		not specified	Likely benign (Jul 03, 2017)
17-40819075-T-TAGCCGCCGCC			Uncertain significance (-)
17-40819076-GG-AGCCACCGCCGGAGCTT			Likely benign (Jul 28, 2017)
17-40819077-GCCGCCGCCGGAGCTT-G			Uncertain significance (Apr 07, 2022)
17-40819077-G-GAGCTT			Benign (May 04, 2021)
17-40819077-G-GCCGCCGCCGGAGCTT			Conflicting classifications of pathogenicity (Apr 08, 2022)
17-40819077-G-GCCGCCGCCGGAGCTTCCGCCGCCGGAGCTT		not specified	Likely benign (May 18, 2017)
17-40819084-C-CG			not provided (-)
17-40819085-C-CG		Congenital reticular ichthyosiform erythroderma	Pathogenic (Oct 01, 2010)
17-40819087-G-T			Uncertain significance (Feb 18, 2023)
17-40819089-GCTT-G		KRT10-related disorder	Likely benign (Feb 01, 2024)
17-40819113-G-T			Likely benign (Mar 16, 2023)
17-40819117-T-G			Likely benign (Oct 03, 2023)
17-40819118-AGCCGCCGCCGAAAC-T		Congenital reticular ichthyosiform erythroderma	Pathogenic (Sep 08, 2021)
17-40819118-A-AGCCGCCGCCGAAACTTCC			Uncertain significance (Nov 24, 2023)
17-40819122-G-T			Benign (Mar 03, 2015)
17-40819128-G-A			Likely benign (Jan 12, 2024)
17-40819144-C-T			Uncertain significance (Jun 13, 2023)
17-40819146-T-G			Likely benign (Mar 16, 2023)
17-40819156-C-T			Uncertain significance (Jul 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KRT10-AS1	protein_coding	protein_coding	ENST00000301665	1	17165

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.617	157	137	1.15	0.00000684	1646
Missense in Polyphen		16	13.678	1.1698		132
Synonymous	-0.807	63	55.4	1.14	0.00000308	549
Loss of Function

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish
East Asian
Finnish
European (Non-Finnish)
Middle Eastern
South Asian
Other

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.810
• rvis_EVS: 0.46
• rvis_percentile_EVS: 78.46

Haploinsufficiency Scores

• pHI: 0.0504
• hipred: N
• hipred_score: 0.146
• ghis: 0.414

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.197

Gene Damage Prediction

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

Gene ontology

• Cellular component: integral component of membrane