MSH5-SAPCD1

MSH5-SAPCD1 readthrough (NMD candidate)

Basic information

Region (hg38): 6:31740019-31764851

Previous symbols: [ "MSH5-C6orf26" ]

Links

ENSG00000255152 ∙ NCBI:100532732 ∙ ∙ HGNC:41994 ∙ ∙ ∙ 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 MSH5-SAPCD1 gene.

• Inborn genetic diseases (33 variants)
• not provided (5 variants)
• not specified (4 variants)
• Spermatogenic failure 74 (4 variants)
• Non-obstructive azoospermia (3 variants)
• MSH5-related condition (1 variants)
• Genetic non-acquired premature ovarian failure (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MSH5-SAPCD1 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			3			3
non coding	2	2	27	6	6	43
Total	2	2	27	6	6

Highest pathogenic variant AF is 0.0000197

Variants in MSH5-SAPCD1

This is a list of pathogenic ClinVar variants found in the MSH5-SAPCD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-31740525-C-A		not specified	Uncertain significance (Jun 28, 2023)
6-31740537-T-TC		Non-obstructive azoospermia • Spermatogenic failure 74	Pathogenic (May 26, 2020)
6-31740551-C-T		not specified • MSH5-related disorder	Benign (Jul 24, 2019)
6-31741167-A-G		not specified	Uncertain significance (Jan 23, 2023)
6-31741212-A-G		not specified	Uncertain significance (May 24, 2023)
6-31741261-C-G		not specified	Uncertain significance (Oct 27, 2021)
6-31741268-C-T		MSH5-related disorder	Benign (Oct 17, 2019)
6-31741276-T-G		MSH5-related disorder	Likely benign (Jun 14, 2019)
6-31742911-G-A		MSH5-related disorder	Benign/Likely benign (Sep 24, 2019)
6-31743119-C-G		not specified	Uncertain significance (Nov 18, 2022)
6-31743949-T-C		not specified	Uncertain significance (Jan 03, 2024)
6-31743963-A-G		not specified	Uncertain significance (Mar 01, 2024)
6-31744014-T-C		not specified	Uncertain significance (Jan 10, 2022)
6-31744026-G-A		Azoospermia	Pathogenic (Dec 20, 2021)
6-31744133-C-T		MSH5-related disorder	Likely benign (Sep 12, 2019)
6-31744194-G-A		Premature ovarian failure 13	Uncertain significance (Mar 26, 2024)
6-31744226-C-G		not specified	Uncertain significance (Dec 15, 2022)
6-31744238-G-A		not specified	Uncertain significance (Jun 06, 2023)
6-31744560-A-G		not specified	Likely benign (Jan 09, 2024)
6-31753314-C-T		Genetic non-acquired premature ovarian failure	Likely pathogenic (Oct 01, 2019)
6-31753364-G-T		not specified	Uncertain significance (Nov 30, 2021)
6-31753437-C-T		not specified	Uncertain significance (Feb 23, 2023)
6-31753579-C-T		Non-obstructive azoospermia • Spermatogenic failure 74	Likely pathogenic (May 09, 2021)
6-31753596-C-A		not specified	Uncertain significance (Oct 14, 2023)
6-31753609-G-A		not specified	Uncertain significance (Aug 22, 2023)

GnomAD

Source: gnomAD

dbNSFP

Source: dbNSFP

Essentials

• gene_indispensability_pred: N
• gene_indispensability_score: 0.114