KRT31

protein-coding

keratin 31, the group of Keratins, type I

Gene summary

The protein encoded by this gene is a member of the keratin gene family. As a type I hair keratin, it is an acidic protein which heterodimerizes with type II keratins to form hair and nails. The type I hair keratins are clustered in a region of chromosome 17q12-q21 and have the same direction of transcription. [provided by RefSeq, Jul 2008]

Previous symbols:

KRTHA1

MANE transcript

NM_002277.3

Inheritance

—

ClinVar variants

U:53B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.36

Max pathogenic AF

—

Genomic locus

chr17:41,393,721-41,397,608

External References & Databases

Ensembl (ENSG00000094796)

Transcript & Mutation Effects

hg38 • Region Span ~3.9 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 KRT31 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 57

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_002277.3. 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	1 clinvar	3
missense			53 clinvar	3 clinvar		56
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	53	5	1	59

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 3 of 3 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_002277.3	RefSeq	NP_002268.2	7	MANE Select
ENST00000251645.3	Ensembl	ENSP00000251645.2	7	MANE Select
ENST00001135910.1	Ensembl	ENSP00000802573.1	7	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Estrogen signaling pathway - Homo sapiens (human)
Keratinization
Developmental Biology

Biological Process

cytoskeleton organization
epidermis development
keratinization
cornification

Molecular Function

structural constituent of cytoskeleton
protein binding

Cellular Component

extracellular space
cytosol
intermediate filament
extracellular exosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000251645
Coding exons: 7
Length: 3869
Individuals with no LoFs: 121375
Homozygous LoFs: 70
Heterozygous LoFs: 4303
Defined: 125748
p: 0.0175

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.186	271	263	1.03	0.0000181	2707
Missense (PolyPhen)		94	95.021	0.98926		1047
Synonymous	-1.34	134	116	1.16	0.00000765	843
Loss of Function	2.61	7	19.4	0.361	9.20e-7	209

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0050	0.0050	notable
Latino/Admixed American	0.0076	0.0075	notable
Ashkenazi Jewish	0.030	0.030	notable
East Asian	0.000054	0.000054	rare
Finnish	0.0074	0.0074	notable
European (Non-Finnish)	0.028	0.028	notable
South Asian	0.0094	0.0093	notable
Other	0.017	0.017	notable

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.209

Intolerance Scores

LoFtool: 0.142
RVIS EVS: 0.16
RVIS percentile EVS: 64.82

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.794

Gene Damage Prediction

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