SLC44A5

solute carrier family 44 member 5, the group of Solute carrier family 44

Basic information

Region (hg38): 1:75202128-75611114

Links

ENSG00000137968 ∙ NCBI:204962 ∙ ∙ HGNC:28524 ∙ Uniprot:Q8NCS7 ∙ 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 SLC44A5 gene.

• Inborn genetic diseases (18 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC44A5 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			16	2		18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	16	2	0

Variants in SLC44A5

This is a list of pathogenic ClinVar variants found in the SLC44A5 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-75206629-A-G		not specified	Uncertain significance (Jul 14, 2021)
1-75206641-T-C		not specified	Uncertain significance (Dec 26, 2023)
1-75206702-T-A		not specified	Uncertain significance (Jul 08, 2022)
1-75213707-G-C		not specified	Uncertain significance (Nov 14, 2023)
1-75213751-A-G		not specified	Uncertain significance (Aug 17, 2022)
1-75213791-C-T		not specified	Likely benign (Aug 02, 2021)
1-75213922-T-C		not specified	Uncertain significance (Feb 09, 2023)
1-75213949-G-C		not specified	Uncertain significance (Jan 03, 2024)
1-75214629-T-C		not specified	Uncertain significance (Apr 13, 2023)
1-75215834-A-G		not specified	Uncertain significance (Aug 06, 2021)
1-75218608-C-T		not specified	Uncertain significance (May 25, 2022)
1-75218734-T-C		not specified	Uncertain significance (Aug 12, 2021)
1-75219283-G-C		not specified	Uncertain significance (Dec 01, 2023)
1-75219803-G-A		not specified	Uncertain significance (Sep 29, 2023)
1-75219843-T-A		not specified	Uncertain significance (Jul 11, 2023)
1-75219860-T-C		not specified	Uncertain significance (Sep 22, 2023)
1-75222445-A-G		not specified	Uncertain significance (Aug 02, 2021)
1-75227782-C-T		not specified	Uncertain significance (Jan 24, 2023)
1-75227815-C-T		not specified	Likely benign (Apr 26, 2023)
1-75234027-A-T		not specified	Uncertain significance (Jan 16, 2024)
1-75238549-C-A		not specified	Uncertain significance (Jan 23, 2024)
1-75242021-G-A		not specified	Uncertain significance (Feb 07, 2023)
1-75242024-G-T		not specified	Uncertain significance (Oct 05, 2023)
1-75242051-T-C		not specified	Uncertain significance (Oct 05, 2023)
1-75251260-G-A		not specified	Uncertain significance (May 16, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC44A5	protein_coding	protein_coding	ENST00000370855	23	408986

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000768	1.00	125705	0	40	125745	0.000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.18	314	379	0.830	0.0000186	4715
Missense in Polyphen		80	128.04	0.62478		1696
Synonymous	0.0531	131	132	0.994	0.00000657	1327
Loss of Function	4.17	16	46.8	0.342	0.00000253	548

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000265	0.000265
Ashkenazi Jewish	0.0000994	0.0000992
East Asian	0.00	0.00
Finnish	0.000510	0.000508
European (Non-Finnish)	0.000168	0.000158
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.000165	0.000163

dbNSFP

Source: dbNSFP

• Pathway: Choline metabolism in cancer - Homo sapiens (human);Metabolism of lipids;Amine compound SLC transporters;Metabolism;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: 0.0966

Intolerance Scores

• loftool: 0.679
• rvis_EVS: -0.29
• rvis_percentile_EVS: 33.34

Haploinsufficiency Scores

• pHI: 0.175
• hipred: Y
• hipred_score: 0.543
• ghis: 0.468

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0965

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc44a5
• Phenotype: hematopoietic system phenotype

Gene ontology

• Biological process: phosphatidylcholine biosynthetic process;choline transport;transmembrane transport
• Cellular component: plasma membrane;integral component of membrane
• Molecular function: choline transmembrane transporter activity