HSDL2-AS1

HSDL2 antisense RNA 1, the group of Antisense RNAs

Basic information

Region (hg38): 9:112399183-112487204

Previous symbols: [ "C9orf147" ]

Links

ENSG00000230185 ∙ NCBI:100133204 ∙ ∙ HGNC:31438 ∙ ∙ ∙ 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-AS1 gene.

• Inborn genetic diseases (6 variants)
• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HSDL2-AS1 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						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			6		3	9
Total	0	0	6	0	3

Variants in HSDL2-AS1

This is a list of pathogenic ClinVar variants found in the HSDL2-AS1 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-AS1	protein_coding	protein_coding	ENST00000457681	3	53389

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.645	0.331	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0175	42	42.3	0.992	0.00000191	885
Missense in Polyphen		0	0.84217	0		80
Synonymous	-0.373	19	17.0	1.11	8.63e-7	316
Loss of Function	1.69	0	3.34	0.00	1.47e-7	45

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

Haploinsufficiency Scores

• ghis: 0.416