Is SLC7A5 p.Val44= (c.132G>C) pathogenic?

SLC7A5 p.Val44= (c.132G>C) is classified Likely benign in SLC7A5 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-03-01). Very rare (popmax 8.48e-05%, nfe).

How common is SLC7A5 p.Val44= (c.132G>C) in the general population?

SLC7A5 p.Val44= (c.132G>C) is very rare (popmax 8.48e-05%, nfe) (gnomAD).

SLC7A5 p.Val44=

c.132G>C · rs2508407597 · VCV2646965

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 8.48e-05%, nfe)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.32	GERP -2.1, phastCons 0.76
Overall
CADD	7.678	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 8.48e-05% European (non-Finnish) · 1/1,179,784 alleles

Overall 6.2e-05% 1/1,611,808 alleles · very rare exomes 1/1,459,450 · genomes 0/152,358 · joint denominator

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: SLC7A5
Protein: p.Val44=
Coding: c.132G>C
MANE Select: NM_003486
dbSNP: rs2508407597
Type: single nucleotide variant
Location: chr16:87869291 (GRCh38)
Gene constraint: LOEUF 0.609 · pLI 0.29 (gnomAD)
Structure: AlphaFold pLDDT 86.44 · 21 PDB

Full SLC7A5 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

SLC7A5 c.1043+6C>T Benign ★★ same type
SLC7A5 p.Ala199= Benign ★★ same type
SLC7A5 p.Asn230Lys Benign ★★ same type
SLC7A5 p.Asp223Val Benign ★★ same type
SLC7A5 p.Ala16Thr Uncertain significance ★ ⚠ same type
SLC7A5 p.Ala193Thr Uncertain significance ★ ⚠ same type
SLC7A5 p.Ala2Val Uncertain significance ★ ⚠ same type
SLC7A5 p.Ala32Ser Uncertain significance ★ ⚠ same type

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/slc7a5-p-val44 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown