SMIM10

small integral membrane protein 10

Basic information

Region (hg38): X:134990991-134992473

Previous symbols: [ "CXorf69" ]

Links

ENSG00000184785 ∙ NCBI:644538 ∙ ∙ HGNC:41913 ∙ Uniprot:Q96HG1 ∙ 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 SMIM10 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SMIM10 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			5			5
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	5	0	0

Variants in SMIM10

This is a list of pathogenic ClinVar variants found in the SMIM10 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-134991127-G-C		not specified	Uncertain significance (Feb 24, 2025)
X-134991139-G-A		not specified	Uncertain significance (Feb 05, 2024)
X-134991166-G-C		not specified	Uncertain significance (Feb 02, 2024)
X-134991177-C-T		not specified	Uncertain significance (May 09, 2023)
X-134991201-C-T		not specified	Uncertain significance (Feb 22, 2023)
X-134991277-G-T		not specified	Uncertain significance (Oct 26, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SMIM10	protein_coding	protein_coding	ENST00000330288	1	1534

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.316	0.500	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.813	19	31.9	0.595	0.00000210	515
Missense in Polyphen		6	11.395	0.52656		202
Synonymous	0.930	11	15.7	0.701	0.00000106	195
Loss of Function	0.531	0	0.328	0.00	2.07e-8	7

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	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Haploinsufficiency Scores

• ghis: 0.515

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S

Gene Damage Prediction

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

Gene ontology

• Cellular component: integral component of membrane