TMEM250

transmembrane protein 250

Basic information

Region (hg38): 9:136114581-136118875

Previous symbols: [ "C9orf69" ]

Links

ENSG00000238227

∙ NCBI:90120 ∙ ∙ HGNC:31009 ∙ Uniprot:H0YL14 ∙ 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 TMEM250 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMEM250 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			2 clinvar			2
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	2	0	0

Variants in TMEM250

This is a list of pathogenic ClinVar variants found in the TMEM250 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-136116519-C-T		not specified	Uncertain significance (Jul 13, 2021)	3179293
9-136116626-C-T		not specified	Uncertain significance (Oct 12, 2021)	3179292

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMEM250	protein_coding	protein_coding	ENST00000418388	1	4305

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.201	0.659	123868	0	15	123883	0.0000605

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.03	78	108	0.722	0.00000859	865
Missense in Polyphen		26	35.099	0.74076		311
Synonymous	-1.98	72	53.6	1.34	0.00000428	323
Loss of Function	0.990	1	2.78	0.360	1.19e-7	27

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000227	0.000225
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000810	0.0000804
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.000167	0.000166

dbNSFP

Source: dbNSFP

Function: FUNCTION: May play a role in cell proliferation by promoting progression into S phase. {ECO:0000269|PubMed:21667337}.;

Haploinsufficiency Scores

pHI
hipred: N
hipred_score: 0.314
ghis: 0.459

Mouse Genome Informatics

Gene name: Tmem250-ps
Phenotype

Gene ontology

Biological process: positive regulation of cell population proliferation;viral process;positive regulation of viral process;cytoskeleton-dependent cytokinesis
Cellular component: nucleus;nucleoplasm;cytoplasm;septin ring;microtubule cytoskeleton;integral component of membrane;septin complex
Molecular function: GTPase activity;protein binding;protein-containing complex scaffold activity