SPEM1

spermatid maturation 1

Basic information

Region (hg38): 17:7420324-7421632

Previous symbols: [ "C17orf83" ]

Links

ENSG00000181323 ∙ NCBI:374768 ∙ OMIM:615116 ∙ HGNC:32429 ∙ Uniprot:Q8N4L4 ∙ 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 SPEM1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPEM1 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			37	6	1	44
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	37	6	1

Variants in SPEM1

This is a list of pathogenic ClinVar variants found in the SPEM1 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-7420392-T-C		not specified	Uncertain significance (Jul 30, 2024)
17-7420393-G-C		not specified	Uncertain significance (Nov 08, 2022)
17-7420427-C-G		not specified	Uncertain significance (May 02, 2024)
17-7420449-G-T		not specified	Uncertain significance (Mar 19, 2024)
17-7420457-C-G		not specified	Uncertain significance (Jan 31, 2024)
17-7420485-G-T		not specified	Uncertain significance (Nov 09, 2022)
17-7420502-A-G			Likely benign (Apr 01, 2024)
17-7420634-G-T		not specified	Uncertain significance (Nov 18, 2022)
17-7420643-G-A		not specified	Uncertain significance (Dec 17, 2023)
17-7420661-T-C		not specified	Uncertain significance (Jun 21, 2021)
17-7420932-A-G		not specified	Uncertain significance (Nov 08, 2022)
17-7420980-T-C		not specified	Uncertain significance (Jul 12, 2022)
17-7420989-C-T		not specified	Uncertain significance (Aug 23, 2021)
17-7420998-C-A		not specified	Uncertain significance (Jan 16, 2024)
17-7421006-C-A		not specified	Uncertain significance (Dec 08, 2023)
17-7421012-C-T		not specified	Uncertain significance (Sep 26, 2023)
17-7421015-C-T		not specified	Uncertain significance (Dec 14, 2022)
17-7421016-G-A		not specified	Likely benign (Nov 09, 2021)
17-7421030-A-C		not specified	Uncertain significance (May 13, 2024)
17-7421033-C-T		not specified	Uncertain significance (May 14, 2024)
17-7421034-G-A		not specified	Likely benign (Apr 28, 2022)
17-7421040-C-T		not specified	Uncertain significance (Dec 09, 2023)
17-7421078-G-A		not specified	Uncertain significance (Jan 17, 2025)
17-7421084-C-T		not specified	Uncertain significance (Feb 27, 2023)
17-7421088-A-G		not specified	Uncertain significance (Jul 31, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPEM1	protein_coding	protein_coding	ENST00000323675	3	1273

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000133	0.637	124778	0	24	124802	0.0000962

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0231	186	187	0.995	0.0000112	1962
Missense in Polyphen		75	81.129	0.92446		915
Synonymous	-0.623	79	72.3	1.09	0.00000411	647
Loss of Function	0.899	9	12.4	0.725	7.68e-7	109

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000123	0.000123
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000465	0.0000464
European (Non-Finnish)	0.000151	0.000150
Middle Eastern	0.00	0.00
South Asian	0.0000980	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for proper cytoplasm removal during spermatogenesis. {ECO:0000250}.

Intolerance Scores

• loftool: 0.200
• rvis_EVS: 0.49
• rvis_percentile_EVS: 79.38

Haploinsufficiency Scores

• pHI: 0.0370
• hipred: N
• hipred_score: 0.173
• ghis: 0.408

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.00110

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Spem1
• Phenotype: reproductive system phenotype

Gene ontology

• Biological process: spermatogenesis;sperm individualization;flagellated sperm motility
• Cellular component: cytoplasm;integral component of membrane