# NM_145167.3(PIGM):c.1042C>T (p.Pro348Ser)

https://sugi.bio/variant/pigm-p-pro348ser

## Summary

**PIGM p.Pro348Ser (c.1042C>T)** is classified **Benign** in PIGM (ClinVar, Single submitter, 1 submitter; last evaluated 2025-10-08). AlphaMissense: ambiguous (0.4844); Low-frequency (popmax 1.76%, sas); Associated with hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency.

**At a glance:** Benign · review: Single submitter · rsID rs201082832 · 1 submitter · 1 linked condition · AlphaMissense ambiguous · low-frequency (popmax 1.76%, sas)

## For patients & families {#patients}

This is a change in the PIGM gene that is classified as benign — not considered disease-causing, submitted by 1 submitter, and is linked to hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency.

*Reference information, not medical advice, and not a prediction for any individual. A genetic counselor or clinician can interpret what it means for you and your family.*

|  |  |
| --- | --- |
| Typical inheritance (of this condition) | Autosomal recessive |
| Age of onset (of this condition) | Infancy, Neonatal |
| Diagnostic panels | PIGM is a diagnostic-grade gene on 9 Genomics England panels |

**Support & next steps:** [Condition overview & support (NIH GARD)](https://rarediseases.info.nih.gov/diseases/0009965/index) · [Find a genetic counselor (NSGC)](https://findageneticcounselor.nsgc.org/).

## Identity {#identity}

| Field | Value |
| --- | --- |
| Gene | [PIGM](https://sugi.bio/atlas/gene/PIGM/) |
| Protein change (HGVS p.) | p.Pro348Ser |
| Coding change (HGVS c.) | c.1042C>T |
| MANE Select transcript | [NM_145167](https://www.ncbi.nlm.nih.gov/nuccore/NM_145167) |
| dbSNP | [rs201082832](https://www.ncbi.nlm.nih.gov/snp/rs201082832/) |
| Variant type | single nucleotide variant |
| Location | chr1:160030698-160030698 (GRCh38) |
| ClinVar | [VCV2056194](https://www.ncbi.nlm.nih.gov/clinvar/variation/2056194/) |

**All HGVS expressions:** `NC_000001.10:g.160000488G>A`, `NC_000001.11:g.160030698G>A`, `NG_012238.1:g.6296C>T`, `NM_145167.3:c.1042C>T`

## Computational & population evidence {#evidence}

**Concordance:** AlphaMissense makes no call; REVEL and SaProt both call this tolerated; AlphaMissense is indeterminate — descriptive only.

- AlphaMissense **ambiguous** (0.4844) — no call either way
- REVEL 0.267 (benign-leaning)
- SaProt LLR -8.056 (tolerated)
- → **In-silico consensus:** REVEL and SaProt both call this tolerated; AlphaMissense is indeterminate
- Conservation: phyloP 9.66, GERP 2.42, phastCons 1 — highly conserved
- CADD: **PHRED 23.0**. No single ClinGen-calibrated threshold exists and the expert panels that use CADD disagree — GUCY2D/AIPL1 require ≥ 20.0 for an untranslated-region variant, ABCA4 ≥ 28.1 for a synonymous or indel variant, the Pulmonary Hypertension panel imports Pejaver 2022's missense-calibrated numbers, and the Antibody Deficiencies panel declines CADD entirely for PIK3CD. CADD v1.7 also incorporates Zoonomia phyloP, so it partly re-expresses the conservation above. *Descriptive; no threshold applied.*
- Regional missense constraint: **o/e 0.98** across the covering region of the MANE Select transcript (160,030,471–160,031,739), spanning 1,268 bp. Chi-square p 0.65. Describes the region, not this allele; gnomAD v4.1.1's own constrained determination. *Descriptive; no ACMG code applied.*
- SpliceAI: **not assessed** — no allele at this position is in our SpliceAI release, either because it lies outside the scored MANE transcript scope or because every allele is below Δ0.2. We cannot tell which, so this claims neither; absence is not evidence against a splicing effect.
- Population frequency (gnomAD v4.1): grpmax **1.76%** (sas) · FAF95 1.69% · FAF99 1.66% · 1,601/91,074 in the highest group · 1,666/1,614,062 alleles overall — low-frequency (popmax 1.76%, sas).

| Ancestry group | Allele frequency | 1 in |
| --- | --- | --- |
| South Asian (grpmax) | 1.76% | 57 |
| Remaining individuals (not grpmax-eligible) | 0.0864% | 1,158 |
| Middle Eastern | 0.0495% | 2,021 |
| African / African-American | 0.004% | 25,018 |
| European (non-Finnish) | 0.000424% | 235,981 |

*Computational predictors are not independent (ClinGen Variant Classification guidance): AlphaMissense (Cheng et al. 2023) carries the ACMG weight for missense and conservation (phyloP/GERP/phastCons) for non-missense; REVEL (Pejaver-2022 calibrated strength bands) and SaProt (Su et al. 2023, structure-aware, ClinVar-independent protein language model, raw LLR) are shown as orthogonal agreement signals, not additive. For frequency, the gnomAD v4.1 grpmax filtering allele frequency (FAF95) is ClinGen's designated BA1/BS1 input (gnomAD v4 guidance v3.0, June 2025); BA1/BS1 thresholds are disease-specific, not a blanket 5%. Predictions, not a clinical determination.*

## Gene constraint & dosage {#gene-context}

**PIGM** population constraint: LOEUF 0.975, pLI 0.0073014, missense-Z 0.73862. *Lower LOEUF and higher pLI indicate a gene that tolerates loss-of-function poorly; ClinGen dosage is the curated haploinsufficiency call.*

Curated gene–disease validity (ClinGen):

- **congenital disorder of glycosylation** — Limited (AR)

## Protein context {#protein}


AlphaFold model confidence (whole protein): pLDDT 90.10, 76% of residues very-high.

## What this gene does {#gene-function}

*Describes the biological roles of PIGM (the gene this variant disrupts) — not effects measured for this specific variant. A damaging variant is expected to affect these functions and pathways; the degree depends on the variant.*

**How this variant is thought to act:** PIGM's established molecular role includes dol-P-Man:GlcN-acyl-PI alpha-1,4-mannosyltransferase activity.


### Pathways affected {#pathways}

PIGM participates in **1 Reactome pathway** (⚕ = disease pathway):

| Pathway (Reactome) | Evidence |
| --- | --- |
| [Synthesis of glycosylphosphatidylinositol (GPI)](https://reactome.org/content/detail/R-HSA-162710) | curated |

### Molecular function & processes (GO — experimentally supported) {#go}

**Molecular function:** dol-P-Man:GlcN-acyl-PI alpha-1,4-mannosyltransferase activity.

**Biological process:** GPI anchor biosynthetic process.

## Clinical significance {#significance}

**Benign** — review status Single submitter *(criteria provided, single submitter)*, last evaluated 2025-10-08.

**Submitter consensus:** unanimous (1/1 Benign).

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| Labcorp Genetics (formerly Invitae), Labcorp | Benign | criteria provided, single submitter | clinical testing | 2025-10-08 |

## Associated conditions {#conditions}

[hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency](https://sugi.bio/atlas/disease/hypercoagulability-syndrome-due-to-glycosylphosphatidylinositol-deficiency/).

**Reported phenotype names (ClinVar):** Hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency, GLYCOSYLPHOSPHATIDYLINOSITOL BIOSYNTHESIS DEFECT 1.

## Similar variants {#similar}

Related PIGM variant pages (same residue, condition, or type): [PIGM p.Pro348Ala](/variant/pigm-p-pro348ala), [PIGM p.Met1Thr](/variant/pigm-p-met1thr), [PIGM p.Arg41Gln](/variant/pigm-p-arg41gln), [PIGM p.Arg46Lys](/variant/pigm-p-arg46lys), [PIGM p.Cys317Tyr](/variant/pigm-p-cys317tyr), [PIGM p.Gln334Pro](/variant/pigm-p-gln334pro), [PIGM p.Glu217Gln](/variant/pigm-p-glu217gln), [PIGM p.Gly20Asp](/variant/pigm-p-gly20asp).

### Data sources & attribution {#sources}

ClinVar (NCBI — public domain, built 2026-10-14); gnomAD v4.1 (Broad Institute, built 2026-10-14); AlphaMissense (Cheng et al. 2023, © Google DeepMind — CC BY 4.0, built 2026-01-27); REVEL (Ioannidis et al. 2016 — ODbL, built 2026-07-13); SaProt (Su et al. 2023 — MIT, built 2026-10-14); SpliceAI (Illumina — free for non-commercial use, built 2026-10-13); CADD (Rentzsch et al. 2019, University of Washington — free for non-commercial use, built 2026-10-10); Conservation (phyloP/phastCons/GERP) (UCSC hg38 470-way mammal (Hiller Lab) + Ensembl Compara, built 2026-07-12); gnomAD Non-coding Constraint (Gnocchi) (Chen et al. 2024, Broad Institute — CC0, built 2026-10-11); gnomAD Regional Missense Constraint (Broad Institute — CC0, built 2026-10-13); Pangolin (Zeng & Li 2022 — CC BY 4.0, built 2026-10-11); Repeat regions (UCSC — RepeatMasker, TRF, segmental duplications, built 2026-10-11); ClinGen (ClinGen, built 2026-09-22); UniProt (CC BY 4.0); Reactome / GO (CC BY 4.0, built 2026-09-23); MaveDB (per-record license, built 2026-10-11); CIViC (CC0, built 2026-09-22); Orphanet (Orphanet, built 2026-06-12)

*Primary record: NCBI ClinVar (variation 2056194). Classifications reflect these databases as of the page's build date and may change. Free reference use — not medical advice; consult the primary submitters and a clinician.*