SMIM29

small integral membrane protein 29

Basic information

Region (hg38): 6:34246380-34249108

Previous symbols: [ "C6orf1" ]

Links

ENSG00000186577 ∙ NCBI:221491 ∙ OMIM:611419 ∙ HGNC:1340 ∙ Uniprot:Q86T20 ∙ 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 SMIM29 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SMIM29 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				1		1
missense			5	1		6
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	2	0

Variants in SMIM29

This is a list of pathogenic ClinVar variants found in the SMIM29 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-34246542-G-A		not specified	Likely benign (Jun 18, 2021)
6-34246605-C-T		not specified	Uncertain significance (Aug 30, 2021)
6-34246675-G-A		not specified	Uncertain significance (Oct 12, 2021)
6-34246748-G-A			Likely benign (Mar 01, 2023)
6-34246762-C-A		not specified	Uncertain significance (Jul 09, 2021)
6-34246807-G-A		not specified	Uncertain significance (Sep 17, 2021)
6-34247117-A-G		not specified	Uncertain significance (Sep 17, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SMIM29	protein_coding	protein_coding	ENST00000476320	3	3091

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.624	0.347	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.467	101	88.6	1.14	0.00000439	995
Missense in Polyphen		24	22.017	1.0901		219
Synonymous	-1.14	46	37.2	1.24	0.00000196	351
Loss of Function	1.64	0	3.12	0.00	1.33e-7	35

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

Recessive Scores

• pRec: 0.0801

Intolerance Scores

• rvis_EVS: 0.08
• rvis_percentile_EVS: 60.09

Haploinsufficiency Scores

• pHI: 0.129
• hipred: N
• hipred_score: 0.123
• ghis: 0.493

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Lbh
• Phenotype: integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); endocrine/exocrine gland phenotype; reproductive system phenotype; normal phenotype

Gene ontology

• Cellular component: integral component of membrane