HSDL1

hydroxysteroid dehydrogenase like 1, the group of Short chain dehydrogenase/reductase superfamily

Basic information

Region (hg38): 16:84122140-84145192

Links

ENSG00000103160 ∙ NCBI:83693 ∙ OMIM:619067 ∙ HGNC:16475 ∙ Uniprot:Q3SXM5 ∙ 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 HSDL1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HSDL1 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						0
missense			17	1		18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1	2	3
Total	0	0	17	2	2

Variants in HSDL1

This is a list of pathogenic ClinVar variants found in the HSDL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-84124638-T-G		not specified	Uncertain significance (Apr 29, 2024)
16-84124641-A-G		not specified	Uncertain significance (Sep 29, 2023)
16-84124667-C-T		not specified	Uncertain significance (Apr 20, 2024)
16-84124680-T-C		not specified	Uncertain significance (Jul 12, 2022)
16-84129571-C-T		not specified	Uncertain significance (Jul 06, 2021)
16-84129616-C-T		not specified	Uncertain significance (Sep 17, 2021)
16-84129715-C-A		not specified	Uncertain significance (Jun 06, 2022)
16-84130010-C-G		not specified	Uncertain significance (Mar 06, 2023)
16-84130064-C-G		not specified	Uncertain significance (Mar 23, 2023)
16-84130111-C-T		not specified	Uncertain significance (Sep 27, 2022)
16-84130116-G-C		not specified	Uncertain significance (May 23, 2023)
16-84130119-A-G		not specified	Uncertain significance (May 25, 2022)
16-84130150-C-T		not specified	Uncertain significance (Oct 05, 2022)
16-84130153-C-T		not specified	Uncertain significance (Apr 18, 2023)
16-84130357-G-A		not specified	Uncertain significance (Feb 11, 2022)
16-84131159-G-A		not specified	Uncertain significance (Aug 17, 2021)
16-84131165-T-C		not specified	Uncertain significance (Sep 14, 2022)
16-84131199-G-C		not specified	Uncertain significance (May 30, 2024)
16-84131201-T-C		not specified	Likely benign (Feb 05, 2024)
16-84131224-G-A		not specified	Uncertain significance (May 13, 2024)
16-84131268-G-C		not specified	Uncertain significance (Oct 04, 2022)
16-84145042-A-G			Benign (Nov 11, 2018)
16-84145087-C-G			Benign (Mar 25, 2019)
16-84145122-G-C			Likely benign (Feb 02, 2021)
16-84145190-C-G			Likely benign (Apr 04, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HSDL1	protein_coding	protein_coding	ENST00000219439	4	22912

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00341	0.956	125736	0	12	125748	0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.08	233	191	1.22	0.0000112	2154
Missense in Polyphen		33	48.482	0.68066		580
Synonymous	-4.06	118	73.7	1.60	0.00000500	655
Loss of Function	1.79	6	12.9	0.464	6.16e-7	159

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000145	0.000145
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.0000264	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Pathway: miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase (Consensus)

Recessive Scores

• pRec: 0.112

Intolerance Scores

• loftool: 0.254
• rvis_EVS: -0.51
• rvis_percentile_EVS: 21.41

Haploinsufficiency Scores

• pHI: 0.214
• hipred: N
• hipred_score: 0.350
• ghis: 0.585

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.464

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hsdl1

Gene ontology

• Cellular component: mitochondrion