SHCBP1L

SHC binding and spindle associated 1 like

Basic information

Region (hg38): 1:182899865-182953525

Previous symbols: [ "C1orf14" ]

Links

ENSG00000157060 ∙ NCBI:81626 ∙ OMIM:619514 ∙ HGNC:16788 ∙ Uniprot:Q9BZQ2 ∙ AlphaFold ∙ 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 SHCBP1L gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SHCBP1L 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			66	5		71
nonsense						0
start loss						0
frameshift						0
inframe indel				1		1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	66	6	0

Variants in SHCBP1L

This is a list of pathogenic ClinVar variants found in the SHCBP1L region.

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

Position	Type	Phenotype	Significance	ClinVar
1-182900020-G-T		not specified	Uncertain significance (Nov 24, 2024)
1-182900047-A-G		not specified	Uncertain significance (Aug 08, 2022)
1-182900117-T-C		not specified	Uncertain significance (Jun 06, 2023)
1-182900125-T-G		not specified	Uncertain significance (Dec 10, 2024)
1-182900135-C-T		not specified	Likely benign (Jan 03, 2022)
1-182900177-A-G		not specified	Uncertain significance (Oct 26, 2021)
1-182900188-C-T		not specified	Likely benign (May 26, 2023)
1-182903064-C-T		not specified	Uncertain significance (Sep 29, 2023)
1-182903094-T-C		not specified	Uncertain significance (Jun 12, 2023)
1-182904185-C-T		not specified	Uncertain significance (Dec 15, 2023)
1-182904205-G-A		not specified	Uncertain significance (Jun 01, 2023)
1-182904263-T-C		not specified	Likely benign (May 17, 2023)
1-182904302-C-T		not specified	Uncertain significance (Nov 09, 2022)
1-182904319-C-T		not specified	Uncertain significance (Nov 27, 2024)
1-182904340-T-C		not specified	Uncertain significance (Jul 12, 2022)
1-182904355-T-C		not specified	Uncertain significance (May 09, 2023)
1-182904392-G-T		not specified	Uncertain significance (Nov 13, 2024)
1-182904427-A-G			Likely benign (Apr 01, 2022)
1-182905532-T-G		not specified	Uncertain significance (Jul 09, 2021)
1-182905549-C-T		not specified	Uncertain significance (Nov 18, 2022)
1-182905583-A-T		not specified	Uncertain significance (Jan 23, 2024)
1-182929750-A-G		not specified	Uncertain significance (May 05, 2023)
1-182939197-A-G		not specified	Uncertain significance (Jun 29, 2023)
1-182939234-A-G		not specified	Uncertain significance (Nov 07, 2023)
1-182939285-T-C		not specified	Uncertain significance (Apr 15, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SHCBP1L	protein_coding	protein_coding	ENST00000367547	10	53661

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.52e-17	0.00612	125009	9	730	125748	0.00294

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0290	350	352	0.996	0.0000189	4241
Missense in Polyphen		89	101.53	0.87658		1266
Synonymous	1.49	107	129	0.833	0.00000767	1234
Loss of Function	0.0490	26	26.3	0.990	0.00000123	358

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00221	0.00217
Ashkenazi Jewish	0.00497	0.00497
East Asian	0.0307	0.0292
Finnish	0.0000937	0.0000924
European (Non-Finnish)	0.000606	0.000598
Middle Eastern	0.0307	0.0292
South Asian	0.000569	0.000555
Other	0.00197	0.00196

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Testis-specific spindle-associated factor that plays a role in spermatogenesis. In association with HSPA2, participates in the maintenance of spindle integrity during meiosis in male germ cells. {ECO:0000250|UniProtKB:Q3TTP0}.

Intolerance Scores

• rvis_EVS: 0.35
• rvis_percentile_EVS: 74.58

Haploinsufficiency Scores

• pHI: 0.115
• hipred: N
• hipred_score: 0.205

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Shcbp1l
• Phenotype: endocrine/exocrine gland phenotype; cellular phenotype; reproductive system phenotype

Gene ontology

• Biological process: spermatogenesis;cell differentiation;positive regulation of chromosome organization
• Cellular component: cytoplasm;meiotic spindle