SMLR1

small leucine rich protein 1

Basic information

Region (hg38): 6:130827405-130837135

Links

ENSG00000256162 ∙ NCBI:100507203 ∙ ∙ HGNC:44670 ∙ Uniprot:H3BR10 ∙ 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 SMLR1 gene.

• Inborn genetic diseases (5 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SMLR1 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				1		1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	5	1	0

Variants in SMLR1

This is a list of pathogenic ClinVar variants found in the SMLR1 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-130827527-G-A		not specified	Uncertain significance (Mar 30, 2022)
6-130827559-T-C		not specified	Uncertain significance (Sep 17, 2021)
6-130834899-C-T		not specified	Uncertain significance (Jun 06, 2023)
6-130834904-A-T		not specified	Uncertain significance (Dec 03, 2021)
6-130834931-GT-G			Likely benign (Jan 01, 2023)
6-130834939-G-T		not specified	Uncertain significance (Dec 19, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SMLR1	protein_coding	protein_coding	ENST00000541421	2	9730

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	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.178	53	56.8	0.933	0.00000292	687
Missense in Polyphen		11	11.249	0.97786		137
Synonymous	-0.786	31	25.9	1.20	0.00000142	222
Loss of Function	0.981	1	2.76	0.363	1.18e-7	28

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

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Smlr1

Gene ontology

• Cellular component: integral component of membrane
• Molecular function: protein binding