TCHHL1

protein-coding

trichohyalin like 1, the group of S100 fused type protein family

Gene summary

This gene belongs to the S100 fused-type protein (SFTP) gene family, and is located in a cluster of SFTP genes on chromosome 1q21. Several members of this family have been implicated in the development of complex skin disorders. This gene is evolutionarily conserved; its expression appears to be hair-specific and spatially restricted within the distal inner root sheath of the hair follicle. It thus may have an important role in hair morphogenesis. [provided by RefSeq, Aug 2013]

Previous symbols:

S100A17
THHL1

MANE transcript

NM_001008536.2

Inheritance

—

ClinVar variants

U:102B:17

Top phenotype

Bladder exstrophy-epispadias-cloacal exstrophy complex

gnomAD constraint

pLI —, LoF o/e 0

Max pathogenic AF

—

Genomic locus

chr1:152,084,141-152,089,064

External References & Databases

Ensembl (ENSG00000182898)

Transcript & Mutation Effects

hg38 • Region Span ~4.9 kb

Loading mutation effect viewer...

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 TCHHL1 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 111

not providedTotal: 7

Bladder exstrophy-epispadias-cloacal exstrophy complexTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001008536.2. 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			102 clinvar	11 clinvar	3 clinvar	116
nonsense					1 clinvar	1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	102	13	4	119

Loading ClinVar variants...

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_001008536.2	RefSeq	NP_001008536.1	2	MANE Select
ENST00000368806.2	Ensembl	ENSP00000357796.1	2	MANE Select

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

transition metal ion binding

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000368806
Coding exons: 2
Length: 4921
Individuals with no LoFs: 125681
Homozygous LoFs: 0
Heterozygous LoFs: 13
Defined: 125694
p: 0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.537	460	429	1.07	0.0000197	5916
Missense (PolyPhen)		47	41.041	1.1452		736
Synonymous	-1.98	194	162	1.20	0.00000755	1759
Loss of Function	1.53	0	2.71	0.00	1.14e-7	38

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.000064	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00011	0.00011	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000065	0.000062	rare
South Asian	0	0.0	absent
Other	0.00017	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0549

Intolerance Scores

LoFtool: 0.906
RVIS EVS: 0.16
RVIS percentile EVS: 64.92

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0661

Gene Damage Prediction

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