Is EMC1 p.Ala21Pro (c.60_61delinsTC) pathogenic?

EMC1 p.Ala21Pro (c.6061delinsTC) is classified Uncertain significance in EMC1 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-11-24). Absent from gnomAD.

How common is EMC1 p.Ala21Pro (c.60_61delinsTC) in the general population?

EMC1 p.Ala21Pro (c.60_61delinsTC) is absent from gnomAD (gnomAD).

EMC1 p.Ala21Pro

c.60_61delinsTC · rs2151970275 · VCV1470218

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 4.7	GERP 1.7, phastCons 1
Regional constraint	o/e 0.95	unconstrained · MANE · 16 kb · p 0.24 · regional, not allelic

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. 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: EMC1
Protein: p.Ala21Pro
Coding: c.60_61delinsTC
MANE Select: NM_015047
dbSNP: rs2151970275
Type: Indel
Location: chr1:19251449 (GRCh38)
Gene constraint: LOEUF 0.913 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 87.67 · 10 PDB

Full EMC1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

EMC1 p.Ala21Thr Uncertain significance ★★ ⚠ same residue
EMC1 p.Ala21= Likely benign ★ same residue
EMC1 c.1090-18_1090-17delinsAC Uncertain significance ★ same type
EMC1 c.2673-4_2673-3delinsAA Uncertain significance ★ same type
EMC1 p.Ala226Ile Uncertain significance ★ same type
EMC1 p.His786Arg Uncertain significance ★ same type
EMC1 p.Ile114Thr Uncertain significance ★ same type
EMC1 p.Pro831Leu 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/emc1-p-ala21pro (accessed [today's date]).

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