TCHHL1

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

Basic information

Region (hg38): 1:152084140-152089064

Previous symbols: [ "S100A17", "THHL1" ]

Links

ENSG00000182898 ∙ NCBI:126637 ∙ ∙ HGNC:31796 ∙ Uniprot:Q5QJ38 ∙ 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 TCHHL1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TCHHL1 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				2		2
missense			39	3	3	45
nonsense					1	1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	39	5	4

Variants in TCHHL1

This is a list of pathogenic ClinVar variants found in the TCHHL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-152084982-G-C		not specified	Uncertain significance (Oct 06, 2023)
1-152085007-C-T		not specified	Uncertain significance (Jun 22, 2023)
1-152085027-T-A		not specified	Uncertain significance (Aug 28, 2023)
1-152085070-C-T		not specified	Likely benign (Aug 16, 2021)
1-152085130-T-C		not specified	Uncertain significance (Nov 08, 2021)
1-152085149-C-G		not specified	Uncertain significance (Mar 21, 2023)
1-152085273-C-G		not specified	Uncertain significance (Jun 18, 2024)
1-152085275-G-T		not specified	Uncertain significance (Feb 13, 2023)
1-152085277-T-C		not specified	Uncertain significance (Oct 12, 2022)
1-152085317-A-G			Benign (Mar 29, 2018)
1-152085352-C-T		not specified	Uncertain significance (Jun 12, 2023)
1-152085438-A-G			Benign/Likely benign (Mar 01, 2022)
1-152085461-G-T		not specified	Likely benign (Mar 25, 2024)
1-152085668-T-C		not specified	Uncertain significance (Feb 10, 2023)
1-152085677-C-G		not specified	Uncertain significance (Feb 27, 2024)
1-152085706-G-T		not specified	Uncertain significance (Nov 03, 2023)
1-152085734-T-C		not specified	Uncertain significance (Mar 20, 2023)
1-152085737-G-A		not specified	Uncertain significance (Jan 16, 2024)
1-152085737-G-C		not specified	Uncertain significance (Feb 10, 2023)
1-152085740-C-T		not specified	Uncertain significance (Apr 08, 2024)
1-152085788-C-G		not specified	Uncertain significance (Jan 08, 2024)
1-152085814-T-C		not specified	Uncertain significance (Jun 28, 2022)
1-152085922-C-T		not specified	Uncertain significance (Aug 04, 2021)
1-152086048-C-G		not specified	Uncertain significance (Apr 08, 2022)
1-152086087-C-T			Likely benign (Apr 03, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TCHHL1	protein_coding	protein_coding	ENST00000368806	2	4921

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.584	0.378	125681	0	13	125694	0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.537	460	429	1.07	0.0000197	5916
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000126	0.000126
Ashkenazi Jewish	0.00	0.00
East Asian	0.000112	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000646	0.0000616
Middle Eastern	0.000112	0.000109
South Asian	0.00	0.00
Other	0.000167	0.000163

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0549

Intolerance Scores

• loftool: 0.906
• rvis_EVS: 0.16
• rvis_percentile_EVS: 64.92

Haploinsufficiency Scores

• pHI: 0.0382
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0661

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tchhl1

Gene ontology

• Molecular function: transition metal ion binding