MSC-AS1

MSC antisense RNA 1, the group of Antisense RNAs

Basic information

Region (hg38): 8:71828167-72118393

Links

ENSG00000235531 ∙ NCBI:100132891 ∙ ∙ HGNC:48724 ∙ ∙ ∙ 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 MSC-AS1 gene.

• Inborn genetic diseases (50 variants)
• not provided (33 variants)
• Familial episodic pain syndrome with predominantly upper body involvement (17 variants)
• not specified (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MSC-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	1		62	20	13	96
Total	1	0	62	20	13

Variants in MSC-AS1

This is a list of pathogenic ClinVar variants found in the MSC-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
8-71842678-A-G		not specified	Uncertain significance (Apr 20, 2024)
8-71842692-G-A		not specified	Uncertain significance (Nov 30, 2021)
8-71842736-G-T		not specified	Uncertain significance (Apr 28, 2023)
8-71843664-T-C		not specified	Uncertain significance (Dec 14, 2023)
8-71843744-C-G		not specified	Uncertain significance (Aug 08, 2022)
8-71843827-C-A		not specified	Uncertain significance (Jun 28, 2023)
8-71843875-C-T		not specified	Uncertain significance (Feb 08, 2023)
8-71843887-T-C		not specified	Uncertain significance (Nov 22, 2023)
8-71843920-C-A		not specified	Uncertain significance (Aug 12, 2021)
8-71843938-C-T		not specified	Uncertain significance (Apr 13, 2022)
8-71843953-G-A		not specified	Uncertain significance (Dec 20, 2021)
8-71844089-G-C			Likely benign (May 01, 2022)
8-71844091-G-A		not specified	Uncertain significance (Sep 27, 2022)
8-71844142-C-G		not specified	Uncertain significance (Feb 03, 2022)
8-71844158-A-T		not specified	Uncertain significance (Mar 19, 2024)
8-72022916-A-G		not specified	Likely benign (Oct 27, 2023)
8-72023100-A-G		not specified	Uncertain significance (Jan 09, 2024)
8-72023839-T-C		not specified	Uncertain significance (Dec 21, 2022)
8-72023867-TTCTTG-T			Uncertain significance (Jul 23, 2020)
8-72023910-T-C		Familial episodic pain syndrome with predominantly upper body involvement • TRPA1-related disorder	Benign (Sep 10, 2021)
8-72023910-TG-CT			Uncertain significance (Sep 01, 2024)
8-72023917-G-A		TRPA1-related disorder	Likely benign (Sep 01, 2024)
8-72026025-G-A		TRPA1-related disorder	Benign (Aug 01, 2022)
8-72026033-C-T			Uncertain significance (May 27, 2022)
8-72026097-G-C		Familial episodic pain syndrome with predominantly upper body involvement	Benign (Sep 10, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MSC-AS1	protein_coding	protein_coding	ENST00000537896	3	290227

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000695	0.765	125265	0	1	125266	0.00000399

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.779	76	97.7	0.778	0.00000452	1105
Missense in Polyphen
Synonymous	-0.0481	43	42.6	1.01	0.00000199	419
Loss of Function	0.997	6	9.28	0.647	4.16e-7	84

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
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: 0.520