Is MVD p.Ser334= (c.1002G>A) pathogenic?

MVD p.Ser334= (c.1002G>A) is classified Likely benign in MVD (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-06-19). Ultra-rare (popmax 0.0786%, afr); Associated with MVD-related disorder.

What condition is associated with MVD p.Ser334= (c.1002G>A)?

MVD p.Ser334= (c.1002G>A) is associated with MVD-related disorder (ClinVar).

How common is MVD p.Ser334= (c.1002G>A) in the general population?

MVD p.Ser334= (c.1002G>A) is ultra-rare (popmax 0.0786%, afr) (gnomAD).

MVD p.Ser334=

c.1002G>A · rs34657446 · VCV3034091

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0786%, afr)

Conditions

MVD-related disorder

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 -11	GERP -3
Overall
CADD	0.077	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0786% African / African-American · 58/73,770 alleles

Filtering AF 0.0624% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0565%

Overall 0.00501% 80/1,598,396 alleles · ultra-rare exomes 44/1,446,130 · genomes 36/152,266 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.0786%	1,272
Admixed American	0.0214%	4,679
Remaining individualsnot grpmax-eligible	0.0097%	10,304
European (non-Finnish)	0.00034%	293,816

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: MVD
Protein: p.Ser334=
Coding: c.1002G>A
MANE Select: NM_002461
dbSNP: rs34657446
Type: single nucleotide variant
Location: chr16:88654703 (GRCh38)
Gene constraint: LOEUF 1.706 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 92.52 · 1 PDB

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

Disease context

MVD-related disorder

Similar variants

MVD p.Ser334Leu Uncertain significance ★ ⚠ same residue
MVD c.71-2A>C Likely pathogenic same condition
MVD p.Pro379His Uncertain significance ⚠ same condition
MVD c.1014-8T>G Benign same condition
MVD c.604-9C>T Likely benign same condition
MVD p.Arg154Trp Benign ⚠ same condition
MVD p.Phe249Ser Pathogenic ★★ same type
MVD p.Thr120Met 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/mvd-p-ser334 (accessed [today's date]).

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