Is EVC p.Met1Val (c.1A>G) pathogenic?

EVC p.Met1Val (c.1A>G) is classified Likely pathogenic in EVC (ClinVar, Single submitter, 1 submitter; last evaluated 2022-04-09). No allele count reported in gnomAD v4.1 (AN 1,010,186); Associated with Ellis-van Creveld syndrome.

What condition is associated with EVC p.Met1Val (c.1A>G)?

EVC p.Met1Val (c.1A>G) is associated with Ellis-van Creveld syndrome, acrofacial dysostosis, Weyers type (ClinVar).

How common is EVC p.Met1Val (c.1A>G) in the general population?

EVC p.Met1Val (c.1A>G) is no allele count reported in gnomAD v4.1 (AN 1,010,186) (gnomAD).

EVC p.Met1Val

c.1A>G · rs1324604027 · VCV2123597

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

start-loss

predicted LoF

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,010,186)

Conditions

Ellis-van Creveld syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	start-loss	predicted loss-of-function
REVEL	0.221	benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 1.9	GERP 0.1, phastCons 1
Overall
CADD	15.96	PHRED · no single calibrated threshold — expert panels disagree

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,010,186). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: EVC
Protein: p.Met1Val
Coding: c.1A>G
MANE Select: NM_153717
dbSNP: rs1324604027
Type: single nucleotide variant
Location: chr4:5711381 (GRCh38)
Gene constraint: LOEUF 1.134 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 74.49

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

Disease context

Ellis-van Creveld syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: acrofacial dysostosis, Weyers type

Similar variants

EVC p.Met1Leu Pathogenic/Likely pathogenic ★★ same residue
EVC p.Met1Lys Likely pathogenic ★★ same residue
EVC p.Met1Thr Likely pathogenic ★ same residue
EVC p.Met1_Ala7del Likely pathogenic ★★ same residue
EVC c.1098+1G>A Pathogenic/Likely pathogenic ★★ same condition
EVC c.175-2A>G Pathogenic/Likely pathogenic ★★ same condition
EVC c.1777-1G>A Pathogenic/Likely pathogenic ★★ same condition
EVC c.1777-2A>G 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/evc-p-met1val (accessed [today's date]).

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