SPEM2

SPEM family member 2

Basic information

Region (hg38): 17:7425616-7427568

Previous symbols: [ "C17orf74" ]

Links

ENSG00000184560 ∙ NCBI:201243 ∙ ∙ HGNC:27315 ∙ Uniprot:Q0P670 ∙ 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 SPEM2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPEM2 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			7			7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	0	0

Variants in SPEM2

This is a list of pathogenic ClinVar variants found in the SPEM2 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-7426791-T-G		not specified	Uncertain significance (Jun 18, 2021)
17-7426980-G-A		not specified	Uncertain significance (Jul 14, 2021)
17-7427076-G-A		not specified	Uncertain significance (Oct 12, 2021)
17-7427126-C-T		not specified	Uncertain significance (Oct 26, 2021)
17-7427138-C-T		not specified	Uncertain significance (Jul 26, 2021)
17-7427142-G-A		not specified	Uncertain significance (May 08, 2024)
17-7427457-G-A		not specified	Uncertain significance (Aug 02, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPEM2	protein_coding	protein_coding	ENST00000333870	3	1954

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.73e-12	0.0724	124754	0	50	124804	0.000200

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0691	342	338	1.01	0.0000232	3236
Missense in Polyphen		99	89.743	1.1031		804
Synonymous	0.920	117	130	0.897	0.00000794	1064
Loss of Function	0.320	18	19.5	0.922	0.00000111	177

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000245	0.000245
Ashkenazi Jewish	0.00	0.00
East Asian	0.000278	0.000278
Finnish	0.000187	0.000186
European (Non-Finnish)	0.000196	0.000194
Middle Eastern	0.000278	0.000278
South Asian	0.000329	0.000327
Other	0.000495	0.000495

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: 0.67
• rvis_percentile_EVS: 84.68

Haploinsufficiency Scores

• pHI: 0.0383
• hipred: N
• hipred_score: 0.146

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Spem2

Gene ontology

• Cellular component: integral component of membrane