TMEM196

transmembrane protein 196

Basic information

Region (hg38): 7:19719314-19773617

Links

ENSG00000173452 ∙ NCBI:256130 ∙ ∙ HGNC:22431 ∙ Uniprot:Q5HYL7 ∙ 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 TMEM196 gene.

• Inborn genetic diseases (9 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMEM196 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			9
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	0	0

Variants in TMEM196

This is a list of pathogenic ClinVar variants found in the TMEM196 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-19722098-G-T		not specified	Uncertain significance (Jul 12, 2022)
7-19722103-G-C		not specified	Uncertain significance (Dec 19, 2022)
7-19725596-C-T		not specified	Uncertain significance (Aug 02, 2022)
7-19725600-T-C		not specified	Uncertain significance (Dec 21, 2023)
7-19725603-G-A		not specified	Uncertain significance (Feb 26, 2024)
7-19725615-G-A		not specified	Uncertain significance (Apr 05, 2023)
7-19725641-G-A		not specified	Uncertain significance (Feb 13, 2023)
7-19772560-T-C		not specified	Uncertain significance (Jul 25, 2023)
7-19772584-C-G		not specified	Uncertain significance (Mar 20, 2023)
7-19772606-C-T		not specified	Uncertain significance (Nov 09, 2021)
7-19772630-C-A		not specified	Uncertain significance (Sep 01, 2021)
7-19772651-C-G		not specified	Uncertain significance (Nov 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMEM196	protein_coding	protein_coding	ENST00000405764	4	54289

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000421	0.229	125725	0	13	125738	0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.213	82	87.6	0.936	0.00000422	1102
Missense in Polyphen		6	10.951	0.5479		105
Synonymous	-1.48	46	34.9	1.32	0.00000172	356
Loss of Function	-0.109	8	7.67	1.04	4.80e-7	86

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	0.000370	0.000370
European (Non-Finnish)	0.0000265	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.494
• rvis_EVS: 0.06
• rvis_percentile_EVS: 58.26

Haploinsufficiency Scores

• pHI: 0.0877
• hipred: N
• hipred_score: 0.289
• ghis: 0.475

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.427

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tmem196

Gene ontology

• Cellular component: integral component of membrane