FLVCR1

Chr 1AR

FLVCR choline and heme transporter 1

Also known as: AXPC1, FLVCR, MFSD7B, NEDMISH, PCA, PCARP, RETSNS, SLC49A1

The protein functions as a transporter that mediates uptake of choline and ethanolamine for phospholipid biosynthesis and exports heme from cells to prevent toxicity. Mutations cause autosomal recessive neurodevelopmental disorder with microcephaly, absent speech, and hypotonia, as well as retinopathy-sensory neuropathy syndrome. The gene shows moderate constraint against loss-of-function variants (LOEUF 0.668), and clinical manifestations primarily affect the nervous system with early neurodevelopmental impacts.

GeneReviewsOMIMResearchSummary from RefSeq, OMIM, UniProt
LOFmechanismARLOEUF 0.672 OMIM phenotypes
Clinical SummaryFLVCR1
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Gene-Disease Validity (ClinGen)
FLVCR1-related retinopathy with or without ataxia · ARDefinitive

Definitive — sufficient evidence for diagnostic panels

Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
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Clinical Trials
1 active or recruiting trial — potential therapeutic options may be available
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GeneReview available — FLVCR1
Authoritative clinical overview · Recommended first read
Open GeneReview ↗

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

Tolerant — LoF & missense variants common in population
LoF Constraint
0.67LOEUF
pLI 0.001
Z-score 2.77
OE 0.38 (0.230.67)
Tolerant

Typical tolerance to LoF variation

Missense Constraint
0.85Z-score
OE missense 0.86 (0.770.95)
243 obs / 283.3 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.38 (0.230.67)
00.351.4
Missense OE0.86 (0.770.95)
00.61.4
Synonymous OE1.02
01.21.6
LoF obs/exp: 9 / 23.5Missense obs/exp: 243 / 283.3Syn Z: -0.19
Curated Mechanism (G2P)Gene2Phenotype (DDG2P) ↗
definitiveFLVCR1-related ataxia, posterior column, with retinitis pigmentosaLOFAR

Predictions shown for reference only — model trained on dominant genes, not applicable to AR conditions.

DN
0.7034th %ile
GOF
0.77top 25%
LOF
0.2485th %ile

The Badonyi & Marsh prediction model was trained exclusively on dominant disease genes. Predictions are not reliable for genes with autosomal recessive inheritance and are shown at reduced opacity for reference only.

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

0 submitted variants in ClinVar

Protein Context — Lollipop Plot

FLVCR1 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

3D Protein StructureAlphaFold
Clinical Literature
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