SHOC1

shortage in chiasmata 1

Basic information

Region (hg38): 9:111686170-111795008

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.

• 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.

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				3		3
missense			9	2		11
nonsense						0
start loss						0
frameshift	1					1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	1	0	9	5	0

Variants in SHOC1

This is a list of pathogenic ClinVar variants found in the SHOC1 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-111686831-C-T		Spermatogenic failure 75	Pathogenic (Jul 06, 2022)
9-111686859-A-G		Inborn genetic diseases	Uncertain significance (Aug 10, 2021)
9-111691656-T-C		Inborn genetic diseases	Uncertain significance (Sep 27, 2021)
9-111691682-C-T		Inborn genetic diseases	Uncertain significance (Oct 29, 2021)
9-111691869-G-A		Inborn genetic diseases	Uncertain significance (Sep 16, 2021)
9-111691976-G-C		Inborn genetic diseases	Uncertain significance (Nov 09, 2021)
9-111700047-C-A		Inborn genetic diseases	Uncertain significance (Nov 15, 2021)
9-111702214-A-G			Likely benign (Jan 01, 2023)
9-111706628-T-C		Inborn genetic diseases	Likely benign (Jun 22, 2021)
9-111707908-G-A			Likely benign (Sep 01, 2023)
9-111718250-C-T		Spermatogenic failure 75	Pathogenic (Jul 06, 2022)
9-111722436-T-C		Inborn genetic diseases	Uncertain significance (Sep 16, 2021)
9-111727693-G-A		Spermatogenic failure 75	Pathogenic (Jul 06, 2022)
9-111727810-CA-C		Spermatogenic failure 75	Pathogenic (Jul 06, 2022)
9-111727880-T-C			Likely benign (May 01, 2022)
9-111738310-AT-A		Spermatogenic failure 75	Pathogenic (Jul 06, 2022)
9-111738418-ACT-A		Non-obstructive azoospermia	Pathogenic (Aug 23, 2021)
9-111746323-TA-T		Spermatogenic failure 75	Pathogenic (Jul 06, 2022)
9-111756408-G-A			Likely benign (Jan 01, 2023)
9-111758176-C-G		Inborn genetic diseases	Uncertain significance (Jul 20, 2021)
9-111775796-T-C		Inborn genetic diseases	Uncertain significance (Aug 30, 2021)
9-111775808-AGT-A		Spermatogenic failure 75	Pathogenic (Jul 06, 2022)

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