Is ELP1 p.Ser910Ter (c.2729C>A) pathogenic?

ELP1 p.Ser910Ter (c.2729C>A) is classified Pathogenic in ELP1 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-01-04). Very rare (popmax 0.0011%, sas).

How common is ELP1 p.Ser910Ter (c.2729C>A) in the general population?

ELP1 p.Ser910Ter (c.2729C>A) is very rare (popmax 0.0011%, sas) (gnomAD).

ELP1 p.Ser910Ter

c.2729C>A · rs1828552155 · VCV2707272

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

nonsense (stop-gain)

predicted LoF

gnomAD v4.1

Rare

very rare (popmax 0.0011%, sas)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	nonsense (stop-gain)	predicted loss-of-function
NMD	predicted	premature termination codon in exon 25 of 37
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 12	GERP 1.6, phastCons 1
Overall
CADD	48.0	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

Grpmax group 0.0011% South Asian · 1/91,078 alleles

Overall 0.000137% 2/1,461,784 alleles · very rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0011%	91,078
European (non-Finnish)	8.47e-05%	1,179,962

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: ELP1
Protein: p.Ser910Ter
Coding: c.2729C>A
MANE Select: NM_003640
dbSNP: rs1828552155
Type: single nucleotide variant
Location: chr9:108896503 (GRCh38)
Gene constraint: LOEUF 0.803 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 84.31 · 5 PDB
Residue 910: the 'mediates dimerization' region

Full ELP1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

ELP1 p.Ser910= Likely benign ★ same residue
ELP1 c.1361-1G>T Pathogenic/Likely pathogenic ★★ same type
ELP1 c.1361-2A>G Pathogenic/Likely pathogenic ★★ same type
ELP1 c.1461-1G>A Likely pathogenic ★★ same type
ELP1 c.1644-1G>T Likely pathogenic ★★ same type
ELP1 c.1644-2A>C Likely pathogenic ★★ same type
ELP1 c.1854+1G>A Likely pathogenic ★★ same type
ELP1 c.2015-2A>G 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/elp1-p-ser910ter (accessed [today's date]).

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