Is PMPCA p.Ser34fs (c.100del) pathogenic?

PMPCA p.Ser34fs (c.100del) is classified Pathogenic in PMPCA (ClinVar, Single submitter, 1 submitter; last evaluated 2023-11-27). No gnomAD frequency available for this variant.

How common is PMPCA p.Ser34fs (c.100del) in the general population?

PMPCA p.Ser34fs (c.100del) is no gnomAD frequency available for this variant (gnomAD).

PMPCA p.Ser34fs

c.100del · rs2538835230 · VCV2722122

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

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.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 2 of 13
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -0.095	GERP -2.5, phastCons 0.044

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

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: PMPCA
Protein: p.Ser34fs
Coding: c.100del
MANE Select: NM_015160
dbSNP: rs2538835230
Type: Deletion
Location: chr9:136412025 (GRCh38)
Gene constraint: LOEUF 1.111 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 88.46

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

Similar variants

INPP5E p.Gln34Arg Uncertain significance ★ ⚠ same residue
INPP5E p.Gly158fs Pathogenic/Likely pathogenic ★★ same type
INPP5E p.Met1_Ser3del Pathogenic/Likely pathogenic ★★ same type
INPP5E p.Pro15fs Pathogenic ★★ same type
INPP5E p.Val587fs Pathogenic/Likely pathogenic ★★ same type
INPP5E c.1159+16_1159+33del Uncertain significance ★★ same type
INPP5E p.Asn636fs Uncertain significance ★★ same type
INPP5E p.Lys312del 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/pmpca-p-ser34fs (accessed [today's date]).

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