SLC44A1

solute carrier family 44 member 1, the group of Solute carrier family 44|CD molecules

Basic information

Region (hg38): 9:105244621-105439171

Previous symbols: [ "CDW92" ]

Links

ENSG00000070214 ∙ NCBI:23446 ∙ OMIM:606105 ∙ HGNC:18798 ∙ Uniprot:Q8WWI5 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• neurodegeneration, childhood-onset, with ataxia, tremor, optic atrophy, and cognitive decline (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Neurodegeneration, childhood-onset, with ataxia, tremor, optic atrophy, and cognitive decline	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Neurologic; Ophthalmologic	28097321; 31855247
Oral choline treatment did not appear to be beneficial

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLC44A1 gene.

• not provided (1 variants)
• Neurodegeneration, childhood-onset, with ataxia, tremor, optic atrophy, and cognitive decline (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC44A1 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				3	3	6
missense			32	1	1	34
nonsense	1	1				2
start loss						0
frameshift	1					1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				2		2
non coding					2	2
Total	2	1	32	4	6

Variants in SLC44A1

This is a list of pathogenic ClinVar variants found in the SLC44A1 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-105244881-A-G		not specified	Uncertain significance (Apr 09, 2024)
9-105244889-C-T			Likely benign (Dec 01, 2022)
9-105244890-T-A		not specified	Uncertain significance (Aug 02, 2021)
9-105244891-C-T		not specified	Uncertain significance (Feb 27, 2023)
9-105299221-G-T		not specified	Uncertain significance (Mar 25, 2024)
9-105299241-C-T		not specified	Uncertain significance (Apr 06, 2022)
9-105299253-C-T		not specified	Uncertain significance (Dec 01, 2022)
9-105299254-G-A		not specified	Uncertain significance (Oct 12, 2021)
9-105309734-G-A		not specified	Uncertain significance (Feb 22, 2023)
9-105309760-G-A		not specified	Uncertain significance (Jan 05, 2022)
9-105309820-A-G		not specified	Uncertain significance (Mar 01, 2023)
9-105335579-G-A		not specified	Uncertain significance (Sep 27, 2022)
9-105335623-A-G		SLC44A1-related disorder	Likely benign (May 23, 2019)
9-105335661-A-G		not specified	Uncertain significance (Oct 25, 2023)
9-105335666-CTGAG-C		Neurodegeneration, childhood-onset, with ataxia, tremor, optic atrophy, and cognitive decline	Pathogenic (Mar 07, 2021)
9-105335679-A-G		not specified	Uncertain significance (Jun 02, 2024)
9-105335690-G-A		not specified	Uncertain significance (Dec 27, 2022)
9-105348387-C-T		not specified	Uncertain significance (Jun 03, 2022)
9-105348402-A-G		not specified	Uncertain significance (Mar 20, 2024)
9-105348414-T-C		not specified	Uncertain significance (May 16, 2024)
9-105348449-G-A			Likely benign (Nov 01, 2022)
9-105356262-A-G		not specified	Uncertain significance (Mar 20, 2024)
9-105356298-GT-G		Neurodegeneration, childhood-onset, with ataxia, tremor, optic atrophy, and cognitive decline	Pathogenic (Sep 01, 2022)
9-105356339-A-G		not specified	Uncertain significance (Jun 06, 2023)
9-105356390-T-C		SLC44A1-related disorder	Benign (Jun 06, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC44A1	protein_coding	protein_coding	ENST00000374720	16	194550

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.997	0.00324	125736	0	11	125747	0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.73	260	351	0.740	0.0000181	4269
Missense in Polyphen		72	127.55	0.56448		1639
Synonymous	0.385	122	128	0.957	0.00000660	1292
Loss of Function	4.81	4	34.5	0.116	0.00000182	421

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000167	0.000151
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000716	0.0000703
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Choline transporter. May be involved in membrane synthesis and myelin production. {ECO:0000269|PubMed:19357133}.
• Pathway: Choline metabolism in cancer - Homo sapiens (human);sarcosine oncometabolite pathway ;Metabolism of lipids;Amine compound SLC transporters;Metabolism of amino acids and derivatives;Metabolism;Choline catabolism;Transport of bile salts and organic acids, metal ions and amine compounds;Synthesis of PC;SLC-mediated transmembrane transport;Transport of small molecules;Glycerophospholipid biosynthesis;Phospholipid metabolism (Consensus)

Recessive Scores

• pRec: 0.137

Intolerance Scores

• loftool: 0.274
• rvis_EVS: -0.53
• rvis_percentile_EVS: 20.7

Haploinsufficiency Scores

• pHI: 0.234
• hipred: Y
• hipred_score: 0.654
• ghis: 0.547

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.183

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc44a1
• Phenotype: adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); 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); growth/size/body region phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); skeleton phenotype

Gene ontology

• Biological process: phosphatidylcholine biosynthetic process;choline transport;choline catabolic process;transmembrane transport
• Cellular component: nucleoplasm;mitochondrion;mitochondrial outer membrane;plasma membrane;membrane;integral component of membrane;extracellular exosome
• Molecular function: choline transmembrane transporter activity