SMIM9

protein-coding

small integral membrane protein 9

Gene summary

Predicted to be located in plasma membrane. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

CXorf68

MANE transcript

NM_001162936.4

Inheritance

—

ClinVar variants

U:10B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.93

Max pathogenic AF

—

Genomic locus

chrX:154,823,348-154,834,662

External References & Databases

Ensembl (ENSG00000203870)

NCBI Gene (100132963)

Transcript & Mutation Effects

hg38 • Region Span ~11.3 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SMIM9 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 10

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001162936.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			9 clinvar	1 clinvar		10
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	10	1	0	11

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 2 of 2 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001162936.4	RefSeq	NP_001156408.1	3	MANE Select
ENST00000369529.2	Ensembl	ENSP00000358542.1	3	MANE Select

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Cellular Component

plasma membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000369529
Coding exons: 3
Length: 11315
Individuals with no LoFs: 0
Homozygous LoFs: 0
Heterozygous LoFs: 0
Defined: 0
p: 0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.359	24	29.5	0.814	0.00000211	616
Missense (PolyPhen)		2	4.1354	0.48363		104
Synonymous	1.00	7	11.3	0.620	7.65e-7	212
Loss of Function	0.116	3	3.22	0.931	2.72e-7	57

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

RVIS EVS: 0.41
RVIS percentile EVS: 76.56

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N

Gene Damage Prediction

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