KRTAP10-1

protein-coding

keratin associated protein 10-1, the group of Keratin associated proteins

Gene summary

This gene encodes a member of the keratin-associated protein (KAP) family. The KAP proteins form a matrix of keratin intermediate filaments which contribute to the structure of hair fibers. KAP family members appear to have unique, family-specific amino- and carboxyl-terminal regions and are subdivided into three multi-gene families according to amino acid composition: the high sulfur, the ultrahigh sulfur, and the high tyrosine/glycine KAPs. This gene encodes a member of the high sulfur KAP family. It is localized to a cluster of intronless KAPs at 21q22.3 which are located within the introns of the C21orf29 gene. [provided by RefSeq, Jul 2008]

Previous symbols:

KRTAP18-1

MANE transcript

NM_198691.3

Inheritance

—

ClinVar variants

U:67B:14

Top phenotype

Ectodermal dysplasia 14, hair/tooth type with or without hypohidrosis

gnomAD constraint

pLI —, LoF o/e 0.88

Max pathogenic AF

—

Genomic locus

chr21:44,538,981-44,540,195

External References & Databases

Ensembl (ENSG00000215455)

Transcript & Mutation Effects

hg38 • Region Span ~1.2 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to KRTAP10-1 variants in ClinVar

4 Conditions Cataloged

not specifiedTotal: 72

not providedTotal: 6

Ectodermal dysplasia 14, hair/tooth type with or without hypohidrosisTotal: 2

Autosomal recessive nonsyndromic hearing loss 98Total: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_198691.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				2 clinvar		2
missense			67 clinvar	8 clinvar	4 clinvar	79
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	67	10	4	81

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 2 of 2 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_198691.3	RefSeq	NP_941964.2	1	MANE Select
ENST00000400375.1	Ensembl	ENSP00000383226.1	1	MANE Select

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

keratinization

Cellular Component

cytosol
keratin filament

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000400375
Coding exons: 1
Length: 1215
Individuals with no LoFs: 0
Homozygous LoFs: 0
Heterozygous LoFs: 0
Defined: 0
p: 0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-1.39	212	162	1.31	0.0000102	1789
Missense (PolyPhen)		0	0.24584	0		2
Synonymous	-4.43	119	71.4	1.67	0.00000507	564
Loss of Function	0.287	6	6.81	0.881	3.08e-7	81

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: In the hair cortex, hair keratin intermediate filaments are embedded in an interfilamentous matrix, consisting of hair keratin-associated proteins (KRTAP), which are essential for the formation of a rigid and resistant hair shaft through their extensive disulfide bond cross-linking with abundant cysteine residues of hair keratins. The matrix proteins include the high- sulfur and high-glycine-tyrosine keratins.;

Intolerance Scores

LoFtool: 0.664
RVIS EVS: 2.78
RVIS percentile EVS: 99.02

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.114

Gene Damage Prediction

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