KRT71

protein-coding

keratin 71, the group of Keratins, type II

Gene summary

Keratins are intermediate filament proteins responsible for the structural integrity of epithelial cells and are subdivided into epithelial keratins and hair keratins. This gene encodes a protein that is expressed in the inner root sheath of hair follicles. The type II keratins are clustered in a region of chromosome 12q13.[provided by RefSeq, Jun 2009]

MANE transcript

NM_033448.3

Inheritance

ClinVar variants

P:1U:125B:39

Top phenotype

Hypotrichosis 13

gnomAD constraint

pLI —, LoF o/e 0.59

Max pathogenic AF

—

Genomic locus

chr12:52,543,909-52,553,145

External References & Databases

Ensembl (ENSG00000139648)

Transcript & Mutation Effects

hg38 • Region Span ~9.2 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

hypotrichosis 13LIMITED

Inheritance Pattern: AD

Disease ID:MONDO:0014390

Submitter: G2P

hypotrichosis 13MODERATE

Inheritance Pattern: AD

Disease ID:MONDO:0014390

Submitter: PanelApp Australia

isolated familial wooly hair disorderSUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0008686

Submitter: Orphanet

hypotrichosis 13LIMITED

Inheritance Pattern: AD

Disease ID:MONDO:0014390

Submitter: Ambry Genetics

hypotrichosis 13LIMITED

Inheritance Pattern: Unknown

Disease ID:MONDO:0014390

Submitter: Labcorp Genetics (formerly Invitae)

Clinical Genomic Database (CGD)

Hypotrichosis 13AD

Manifestation: Dermatologic

Intervention: General

Rationale: Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing

Refs: 22592156

Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to KRT71 variants in ClinVar

4 Conditions Cataloged

not specifiedTotal: 116

not providedTotal: 86

KRT71-related disorderTotal: 12

Hypotrichosis 13Total: 5

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_033448.3. 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	19 clinvar	6 clinvar	27
missense	1 clinvar		123 clinvar	9 clinvar	5 clinvar	138
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	1	0	125	28	11	165

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 5 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_033448.3	RefSeq	NP_258259.1	9	MANE Select
ENST00000267119.6	Ensembl	ENSP00000267119.5	9	MANE Select
XM_017018749.2	RefSeq	XP_016874238.1	9	Standard
XM_047428196.1	RefSeq	XP_047284152.1	7	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Vitamin D Receptor Pathway
Keratinization
Developmental Biology

Biological Process

hair follicle morphogenesis
keratinization
intermediate filament organization
cornification

Molecular Function

structural molecule activity
protein binding

Cellular Component

cytosol
keratin filament
extracellular exosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000267119
Coding exons: 9
Length: 9239
Individuals with no LoFs: 125696
Homozygous LoFs: 0
Heterozygous LoFs: 52
Defined: 125748
p: 0.000207

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.410	340	319	1.06	0.0000200	3422
Missense (PolyPhen)		121	128.65	0.94051		1486
Synonymous	0.182	134	137	0.980	0.00000877	1045
Loss of Function	1.76	13	21.9	0.595	0.00000112	254

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00074	0.00074	rare
Latino/Admixed American	0.00024	0.00023	rare
Ashkenazi Jewish	0.00030	0.00020	rare
East Asian	0.000054	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00018	0.00018	rare
South Asian	0.00029	0.00029	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Plays a central role in hair formation. Essential component of keratin intermediate filaments in the inner root sheath (IRS) of the hair follicle. {ECO:0000269|PubMed:22592156}.;
Disease: DISEASE: Hypotrichosis 13 (HYPT13) [MIM:615896]: A form of hypotrichosis, a condition characterized by the presence of less than the normal amount of hair and abnormal hair follicles and shafts, which are thin and atrophic. The extent of scalp and body hair involvement can be very variable, within as well as between families. HYPT13 is characterized by sparse woolly hair. {ECO:0000269|PubMed:22592156}. Note=The disease is caused by mutations affecting the gene represented in this entry.;

Recessive Scores

pRec: 0.109

Intolerance Scores

LoFtool: 0.207
RVIS EVS: 1.03
RVIS percentile EVS: 91.09

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.144

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High