Is DYNAP p.Val55Met (c.163G>A) pathogenic?

DYNAP p.Val55Met (c.163G>A) is classified Likely benign in DYNAP (ClinVar, Single submitter, 1 submitter; last evaluated 2021-12-17). AlphaMissense: likely benign (0.0921); Ultra-rare (popmax 0.0826%, mid).

How common is DYNAP p.Val55Met (c.163G>A) in the general population?

DYNAP p.Val55Met (c.163G>A) is ultra-rare (popmax 0.0826%, mid) (gnomAD).

What do computational predictors say about DYNAP p.Val55Met (c.163G>A)?

AlphaMissense predicts likely benign (score 0.0921) — an in-silico prediction, not a clinical call.

DYNAP p.Val55Met

c.163G>A · rs201631044 · VCV2359627

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0921 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0826%, mid)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0921	likely benign
REVEL	0.013	strongly benign-leaning
SaProt	LLR -7.63	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 -0.41	GERP -3.7
Regional constraint	o/e 1.14	unconstrained · MANE · 6,859 bp · p 0.034 · regional, not allelic
Overall
CADD	2.127	PHRED · no single calibrated threshold — expert panels disagree

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

⚠ Isoform check: AlphaMissense numbered on a different transcript (AM V81M vs ClinVar V55M) — verify the residue.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0826% Middle Eastern · 5/6,052 alleles

Filtering AF 0.0325% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0211%

Overall 0.0197% 317/1,612,762 alleles · ultra-rare

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.0826%	1,210
Remaining individualsnot grpmax-eligible	0.0352%	2,837
Admixed American	0.0317%	3,153
European (non-Finnish)	0.0218%	4,588
East Asian	0.0178%	5,605
African / African-American	0.008%	12,492

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: DYNAP
Protein: p.Val55Met
Coding: c.163G>A
MANE Select: NM_173629
dbSNP: rs201631044
Type: single nucleotide variant
Location: chr18:54595044 (GRCh38)
Gene constraint: LOEUF 1.221 · pLI 0.07 (gnomAD)
Structure: AlphaFold pLDDT 60.24

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

Similar variants

DYNAP c.13A>C Uncertain significance ★ ⚠ same type
DYNAP c.14T>C Uncertain significance ★ same type
DYNAP c.20G>A Uncertain significance ★ ⚠ same type
DYNAP c.28C>A Uncertain significance ★ ⚠ same type
DYNAP c.-29G>C Uncertain significance ★ ⚠ same type
DYNAP p.Ala158Asp Uncertain significance ★ ⚠ same type
DYNAP p.Ala169Thr Uncertain significance ★ ⚠ same type
DYNAP p.Ala29Pro 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/dynap-p-val55met (accessed [today's date]).

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