Is OAT p.Ala370= (c.1110C>T) pathogenic?

OAT p.Ala370= (c.1110C>T) is classified Likely benign in OAT (ClinVar, Multiple submitters, 4 submitters; last evaluated 2025-12-17). Ultra-rare (popmax 0.086%, sas); Associated with ornithine aminotransferase deficiency.

What condition is associated with OAT p.Ala370= (c.1110C>T)?

OAT p.Ala370= (c.1110C>T) is associated with ornithine aminotransferase deficiency (ClinVar).

How common is OAT p.Ala370= (c.1110C>T) in the general population?

OAT p.Ala370= (c.1110C>T) is ultra-rare (popmax 0.086%, sas) (gnomAD).

How is Gyrate atrophy of choroid and retina inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

OAT p.Ala370=

c.1110C>T · rs148325838 · VCV1080234

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.086%, sas)

Conditions

ornithine aminotransferase deficiency

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · G>C here scores Δ0.80 · evaluated, not missing
Constraint at this position
Conservation	phyloP -6.1	GERP -4
Overall
CADD	0.38	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.086% South Asian · 78/90,716 alleles

Filtering AF 0.0706% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0649%

Overall 0.00691% 111/1,605,326 alleles · ultra-rare exomes 98/1,453,428 · genomes 13/151,898 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.086%	1,163
African / African-American	0.012%	8,306
Admixed American	0.00667%	14,988
Remaining individualsnot grpmax-eligible	0.00483%	20,703
East Asian	0.00223%	44,776
Finnishnot grpmax-eligible	0.00157%	63,886
European (non-Finnish)	0.00128%	78,280

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: OAT
Protein: p.Ala370=
Coding: c.1110C>T
MANE Select: NM_000274
dbSNP: rs148325838
Type: single nucleotide variant
Location: chr10:124400889 (GRCh38)
Gene constraint: LOEUF 0.968 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 94.29 · 35 PDB
Residue 370: a β-strand

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

Disease context

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

For Gyrate atrophy of choroid and retina (Orphanet):

Inheritance: Autosomal recessive
Onset: Childhood
Prevalence: 1-9 / 100 000 (Finland)

Similar variants

OAT c.1014+1G>A Likely pathogenic ★★ same condition
OAT c.199+2T>A Likely pathogenic ★★ same condition
OAT c.425-2A>G Pathogenic ★★ same condition
OAT c.520+1G>A Likely pathogenic ★★ same condition
OAT c.648+1G>A Likely pathogenic ★★ same condition
OAT c.772-1G>A Pathogenic/Likely pathogenic ★★ same condition
OAT c.900+1G>A Pathogenic/Likely pathogenic ★★ same condition
OAT p.Arg180Thr Pathogenic/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/oat-p-ala370 (accessed [today's date]).

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