SIGLECL1

SIGLEC family like 1, the group of Ig-like cell adhesion molecule family

Basic information

Region (hg38): 19:51246348-51269330

Previous symbols: [ "C19orf75", "SIGLEC23P", "SIGLECP7" ]

Links

ENSG00000179213 ∙ NCBI:284369 ∙ ∙ HGNC:26856 ∙ Uniprot:Q8N7X8 ∙ 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 SIGLECL1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SIGLECL1 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	3		12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	9	3	0

Variants in SIGLECL1

This is a list of pathogenic ClinVar variants found in the SIGLECL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-51265425-G-C		not specified	Uncertain significance (Dec 11, 2024)
19-51265448-C-A		not specified	Uncertain significance (Sep 16, 2021)
19-51265481-G-A		not specified	Uncertain significance (Apr 26, 2024)
19-51265546-C-G		not specified	Uncertain significance (Dec 06, 2022)
19-51265616-G-A		not specified	Likely benign (Dec 07, 2022)
19-51265643-A-G		not specified	Uncertain significance (Jan 01, 2025)
19-51265777-G-C		not specified	Uncertain significance (Dec 20, 2023)
19-51265778-A-G			Likely benign (Mar 01, 2023)
19-51265807-T-G		not specified	Uncertain significance (Apr 18, 2023)
19-51265822-A-G		not specified	Uncertain significance (Feb 07, 2025)
19-51265837-C-A		not specified	Uncertain significance (Dec 28, 2023)
19-51265852-C-T		not specified	Uncertain significance (Aug 02, 2021)
19-51265861-T-C		not specified	Uncertain significance (Jan 10, 2022)
19-51267501-T-G		not specified	Uncertain significance (Aug 28, 2024)
19-51267503-G-A		not specified	Likely benign (May 11, 2022)
19-51267522-G-A		not specified	Likely benign (Sep 27, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SIGLECL1	protein_coding	protein_coding	ENST00000316401	5	22982

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.69e-8	0.0860	125497	1	248	125746	0.000991

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.718	88	109	0.807	0.00000572	1274
Missense in Polyphen		14	25.758	0.54352		331
Synonymous	0.103	43	43.9	0.980	0.00000261	394
Loss of Function	-0.510	10	8.41	1.19	3.55e-7	102

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000681	0.000681
Ashkenazi Jewish	0.00734	0.00737
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000987	0.000967
Middle Eastern	0.00	0.00
South Asian	0.00126	0.00121
Other	0.00147	0.00147

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: 0.04
• rvis_percentile_EVS: 56.92

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.123
• ghis: 0.384

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: 4931406B18Rik
• Phenotype: normal phenotype

Gene ontology

• Cellular component: integral component of membrane