Is MPC1 p.Asp17Ala (c.50A>C) pathogenic?

MPC1 p.Asp17Ala (c.50A>C) is classified Uncertain significance in MPC1 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-11-07). AlphaMissense: ambiguous (0.3843); Absent from gnomAD v4.1.

How common is MPC1 p.Asp17Ala (c.50A>C) in the general population?

MPC1 p.Asp17Ala (c.50A>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about MPC1 p.Asp17Ala (c.50A>C)?

AlphaMissense predicts ambiguous (score 0.3843) — an in-silico prediction, not a clinical call.

MPC1 p.Asp17Ala

c.50A>C · rs2534084950 · VCV2501431

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.3843 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/2 damaging

REVEL, SaProt · AlphaMissense indeterminate

Computational evidence

Protein change
AlphaMissense	0.3843	ambiguous
REVEL	0.116	moderately benign-leaning
SaProt	LLR -6.82	tolerated
⇒ REVEL and SaProt both call this tolerated; AlphaMissense is indeterminate.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.1	GERP 0.96, phastCons 1
Regional constraint	o/e 1.20	unconstrained · MANE · 13 kb · p 0.24 · regional, not allelic
Overall
CADD	24.4	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

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: MPC1
Protein: p.Asp17Ala
Coding: c.50A>C
MANE Select: NM_016098
dbSNP: rs2534084950
Type: single nucleotide variant
Location: chr6:166382827 (GRCh38)
Gene constraint: LOEUF 0.919 · pLI 0.10 (gnomAD)
Structure: AlphaFold pLDDT 92.85 · 13 PDB
Residue 17: an α-helix

Full MPC1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

MPC1 p.Arg76Gln Uncertain significance ★★ ⚠ same type
MPC1 p.Glu102Lys Uncertain significance ★★ ⚠ same type
MPC1 p.Thr106Met Uncertain significance ★★ ⚠ same type
MPC1 c.72-8C>T Likely benign ★★ same type
MPC1 p.Ala10= Benign/Likely benign ★★ same type
MPC1 p.His101= Benign ★★ same type
MPC1 p.Leu36Ile Benign ★★ same type
MPC1 p.Ala70Thr Likely pathogenic ★ 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/mpc1-p-asp17ala (accessed [today's date]).

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