Is SLC25A13 p.Pro320= (c.960A>G) pathogenic?

SLC25A13 p.Pro320= (c.960A>G) is classified Conflicting classifications of pathogenicity in SLC25A13 (ClinVar, Conflicting submitters, 4 submitters; last evaluated 2026-01-12). Ultra-rare (popmax 0.0817%, amr); Associated with citrin deficiency.

What condition is associated with SLC25A13 p.Pro320= (c.960A>G)?

SLC25A13 p.Pro320= (c.960A>G) is associated with citrin deficiency, citrullinemia (ClinVar).

How common is SLC25A13 p.Pro320= (c.960A>G) in the general population?

SLC25A13 p.Pro320= (c.960A>G) is ultra-rare (popmax 0.0817%, amr) (gnomAD).

SLC25A13 p.Pro320=

c.960A>G · rs765358773 · VCV499617

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 4 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0817%, amr)

Conditions

citrin deficiency

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 -9.1	GERP -3.9
Overall
CADD	0.989	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0817% Admixed American · 49/60,000 alleles

Filtering AF 0.0634% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.057%

Overall 0.00335% 54/1,614,020 alleles · ultra-rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.0817%	1,224
African / African-American	0.00534%	18,730
Remaining individualsnot grpmax-eligible	0.0016%	62,486

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: SLC25A13
Protein: p.Pro320=
Coding: c.960A>G
MANE Select: NM_014251
dbSNP: rs765358773
Type: single nucleotide variant
Location: chr7:96184985 (GRCh38)
Gene constraint: LOEUF 0.937 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 83.09 · 1 PDB

Full SLC25A13 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

citrin deficiency — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: citrullinemia

Similar variants

SLC25A13 c.1177+1G>A Pathogenic ★★ same condition
SLC25A13 c.1178-1G>C Likely pathogenic ★★ same condition
SLC25A13 c.1178-1G>T Likely pathogenic ★★ same condition
SLC25A13 c.1230+1G>C Pathogenic ★★ same condition
SLC25A13 c.1231-1G>A Pathogenic/Likely pathogenic ★★ same condition
SLC25A13 c.1311+1G>A Pathogenic ★★ same condition
SLC25A13 c.1311+1G>C Pathogenic ★★ same condition
SLC25A13 c.1452+1G>A Likely pathogenic ★★ same condition

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/slc25a13-p-pro320 (accessed [today's date]).

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