SHOC1

shortage in chiasmata 1

Basic information

Region (hg38): 9:111686171-111795008

Previous symbols: [ "C9orf84" ]

Links

ENSG00000165181 ∙ NCBI:158401 ∙ OMIM:618038 ∙ HGNC:26535 ∙ Uniprot:Q5VXU9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• spermatogenic failure (Limited), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Spermatogenic failure 75	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Genitourinary	32741963; 32900840; 35485979

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SHOC1 gene.

• Inborn_genetic_diseases (10 variants)
• Spermatogenic_failure_75 (8 variants)
• not_provided (6 variants)
• Male_infertility (4 variants)
• SHOC1-related_condition (1 variants)
• Non-obstructive_azoospermia (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SHOC1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001378211.1. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				4		4
missense	2		10	2		14
nonsense	1	2				3
start loss						0
frameshift	7					7
splice donor/acceptor (+/-2bp)	1					1
Total	11	2	10	6	0

Highest pathogenic variant AF is 0.00004897263

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SHOC1	protein_coding	protein_coding	ENST00000374287	25	108836

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.71e-22	0.942	125650	0	94	125744	0.000374

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.32	582	679	0.857	0.0000312	9488
Missense in Polyphen		134	161.34	0.83056		2339
Synonymous	2.35	197	244	0.809	0.0000115	2588
Loss of Function	2.60	45	68.2	0.660	0.00000304	989

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00169	0.00169
Ashkenazi Jewish	0.00	0.00
East Asian	0.000229	0.000217
Finnish	0.00	0.00
European (Non-Finnish)	0.000208	0.000202
Middle Eastern	0.000229	0.000217
South Asian	0.000284	0.000261
Other	0.000493	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: ATPase required during meiosis for the formation of crossover recombination intermediates (By similarity). Binds DNA: preferentially binds to single-stranded DNA and DNA branched structures (PubMed:29742103). Does not show nuclease activity in vitro, but shows ATPase activity, which is stimulated by the presence of single-stranded DNA (PubMed:29742103). {ECO:0000250|UniProtKB:A2ALV5, ECO:0000269|PubMed:29742103}.

Intolerance Scores

• rvis_EVS: 2.5
• rvis_percentile_EVS: 98.65

Haploinsufficiency Scores

• pHI: 0.142
• hipred: N
• hipred_score: 0.173

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: AI481877
• Phenotype: endocrine/exocrine gland phenotype; cellular phenotype; reproductive system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Gene ontology

• Biological process: resolution of meiotic recombination intermediates
• Cellular component: condensed nuclear chromosome
• Molecular function: single-stranded DNA binding;ATPase activity