Is ASPNAT p.Ala144Val (c.431C>T) pathogenic?

ASPNAT p.Ala144Val (c.431C>T) is classified Likely benign in ASPNAT (ClinVar, Single submitter, 1 submitter; last evaluated 2018-09-19). AlphaMissense: likely benign (0.0814); Rare (popmax 0.196%, afr).

How common is ASPNAT p.Ala144Val (c.431C>T) in the general population?

ASPNAT p.Ala144Val (c.431C>T) is rare (popmax 0.196%, afr) (gnomAD).

What do computational predictors say about ASPNAT p.Ala144Val (c.431C>T)?

AlphaMissense predicts likely benign (score 0.0814) — an in-silico prediction, not a clinical call.

ASPNAT p.Ala144Val

c.431C>T · rs545710012 · VCV712889

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0814 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.196%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0814	likely benign
REVEL	0.023	moderately benign-leaning
SaProt	LLR -6.77	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.17	GERP -3.2, phastCons 0.93
Regional constraint	o/e 0.56	unconstrained · MANE · 3,077 bp · p 8.6e-12 · regional, not allelic
Overall
CADD	13.67	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.196% African / African-American · 146/74,536 alleles

Filtering AF 0.17% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.16%

Overall 0.0106% 170/1,598,672 alleles · rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.196%	511
Remaining individualsnot grpmax-eligible	0.0146%	6,867
Admixed American	0.012%	8,363
European (non-Finnish)	0.000682%	146,694

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: ASPNAT
Protein: p.Ala144Val
Coding: c.431C>T
MANE Select: NM_178557
dbSNP: rs545710012
Type: single nucleotide variant
Location: chr4:2061052 (GRCh38)
Structure: AlphaFold pLDDT 81.36
Residue 144: the n-acetyltransferase domain

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

Similar variants

ASPNAT c.541+8C>T Benign ★★ same type
ASPNAT p.Ala35= Likely benign ★★ same type
ASPNAT p.Gly263= Likely benign ★★ same type
ASPNAT p.Pro56= Likely benign ★★ same type
ASPNAT p.Ala125Thr Uncertain significance ★ ⚠ same type
ASPNAT p.Ala225Thr Uncertain significance ★ ⚠ same type
ASPNAT p.Ala22Val Uncertain significance ★ ⚠ same type
ASPNAT p.Ala255Thr 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/aspnat-p-ala144val (accessed [today's date]).

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