TMEM252

transmembrane protein 252

Basic information

Region (hg38): 9:68536579-68540883

Previous symbols: [ "C9orf71" ]

Links

ENSG00000181778 ∙ NCBI:169693 ∙ ∙ HGNC:28537 ∙ Uniprot:Q8N6L7 ∙ 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 TMEM252 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMEM252 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			9	2		11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	2	0

Variants in TMEM252

This is a list of pathogenic ClinVar variants found in the TMEM252 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-68537285-C-T		not specified	Uncertain significance (Aug 02, 2021)
9-68537317-G-A		not specified	Uncertain significance (Oct 12, 2021)
9-68537386-G-A		not specified	Likely benign (Aug 16, 2021)
9-68537399-G-C		not specified	Uncertain significance (Nov 21, 2022)
9-68537443-T-G		not specified	Uncertain significance (Apr 05, 2023)
9-68537489-C-T		not specified	Uncertain significance (Jan 30, 2024)
9-68540571-C-T		not specified	Uncertain significance (Aug 13, 2021)
9-68540582-C-T		not specified	Uncertain significance (Oct 25, 2023)
9-68540585-A-T		not specified	Uncertain significance (Jun 17, 2024)
9-68540627-T-C		not specified	Uncertain significance (Oct 13, 2023)
9-68540712-C-T		not specified	Likely benign (Aug 12, 2021)
9-68540787-A-G		not specified	Uncertain significance (Jul 14, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMEM252	protein_coding	protein_coding	ENST00000377311	2	4288

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.199	0.659	125442	0	172	125614	0.000685

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.230	99	92.8	1.07	0.00000479	1089
Missense in Polyphen		17	24.556	0.69229		332
Synonymous	-0.679	44	38.6	1.14	0.00000215	362
Loss of Function	0.981	1	2.76	0.363	1.18e-7	33

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00693	0.00695
European (Non-Finnish)	0.000177	0.000176
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000327	0.000326

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: 0.06
• rvis_percentile_EVS: 58.53

Haploinsufficiency Scores

• pHI: 0.0463
• hipred: N
• hipred_score: 0.123
• ghis: 0.386

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tmem252

Gene ontology

• Cellular component: integral component of membrane