HSDL2

hydroxysteroid dehydrogenase like 2, the group of Short chain dehydrogenase/reductase superfamily

Basic information

Region (hg38): 9:112380080-112472405

Previous symbols: [ "C9orf99" ]

Links

ENSG00000119471 ∙ NCBI:84263 ∙ ∙ HGNC:18572 ∙ Uniprot:Q6YN16 ∙ 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 HSDL2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HSDL2 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					1	1
missense			8	1	1	10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	8	1	2

Variants in HSDL2

This is a list of pathogenic ClinVar variants found in the HSDL2 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-112405714-A-T			Benign (Sep 12, 2018)
9-112409009-G-A		not specified	Uncertain significance (Aug 01, 2024)
9-112409029-T-C			Benign (Aug 20, 2018)
9-112416906-C-G		not specified	Uncertain significance (Jan 03, 2024)
9-112438497-A-G		not specified	Uncertain significance (Jan 09, 2024)
9-112438575-T-C		not specified	Uncertain significance (Dec 07, 2023)
9-112438607-G-A		not specified	Likely benign (Feb 28, 2024)
9-112441717-A-C		not specified	Uncertain significance (Jun 07, 2023)
9-112454041-A-G			Benign (Dec 31, 2019)
9-112454063-C-T		not specified	Uncertain significance (Feb 28, 2023)
9-112459464-C-T		not specified	Uncertain significance (Nov 14, 2024)
9-112459486-C-A		not specified	Uncertain significance (Dec 06, 2021)
9-112459567-A-C		not specified	Uncertain significance (Jun 13, 2022)
9-112459574-T-G		not specified	Uncertain significance (Jul 20, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HSDL2	protein_coding	protein_coding	ENST00000398805	11	92474

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000514	0.971	124726	1	66	124793	0.000268

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.904	182	220	0.828	0.0000103	2760
Missense in Polyphen		70	93.158	0.75141		1138
Synonymous	0.672	67	74.4	0.901	0.00000371	770
Loss of Function	1.96	10	19.3	0.518	9.05e-7	262

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000523	0.000521
Ashkenazi Jewish	0.00	0.00
East Asian	0.000223	0.000223
Finnish	0.0000476	0.0000464
European (Non-Finnish)	0.000125	0.000124
Middle Eastern	0.000223	0.000223
South Asian	0.00101	0.000948
Other	0.000671	0.000660

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Has apparently no steroid dehydrogenase activity. {ECO:0000269|PubMed:19703561}.

Recessive Scores

• pRec: 0.118

Intolerance Scores

• loftool: 0.474
• rvis_EVS: 0.02
• rvis_percentile_EVS: 55.22

Haploinsufficiency Scores

• pHI: 0.337
• hipred: N
• hipred_score: 0.284
• ghis: 0.500

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.332

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hsdl2

Gene ontology

• Biological process: biological_process;oxidation-reduction process
• Cellular component: mitochondrion;peroxisome;membrane
• Molecular function: molecular_function;oxidoreductase activity